The NCBI Taxonomy database is a curated set of names and classifications for all of the organisms that are represented in GenBank. When new sequences are submitted to GenBank, the submission is checked for new organism names, which are then classified and added to the Taxonomy database. As of April 2003, there were 176,890 total taxa represented.
There are two main tools for viewing the information in the Taxonomy database: the Taxonomy Browser, and Taxonomy Entrez. Both systems allow searching of the Taxonomy database for names, and both link to the relevant sequence data. However, the Taxonomy Browser provides a hierarchical view of the classification (the best display for most casual users interested in exploring our classification), whereas Entrez Taxonomy provides a uniform indexing, search, and retrieval engine with a common mechanism for linking between the Taxonomy and other relevant Entrez databases.
By the time the NCBI was created in 1988, the nucleotide
sequence databases (GenBank,
The Taxonomy Project started in 1991, in association with
the launch of Entrez (
To represent, manipulate, and store versions of each of the different database taxonomies, we wrote a stand-alone, tree-structured database manager, TaxMan. This also allowed us to merge the taxonomies into a single composite classification. The resulting hybrid was, at first, a bigger mess than any of the pieces had been, but it gave us a starting point that spanned all of the names in all of the sequence databases. For many years, we cleaned up and maintained the NCBI Taxonomy database with TaxMan.
After the initial unification and clean-up of the taxonomy for Entrez was complete, Mitch Sogin organized a workshop to give us advice on the clean-up and recommendations for the long-term maintenance of the taxonomy. This was held at the NCBI in 1993 and included: Mitch Sogin (protists), David Hillis (chordates), John Taylor (fungi), S.C. Jong (fungi), John Gunderson (protists), Russell Chapman (algae), Gary Olsen (bacteria), Michael Donoghue (plants), Ward Wheeler (invertebrates), Rodney Honeycutt (invertebrates), Jack Holt (bacteria), Eugene Koonin (viruses), Andrzej Elzanowski (PIR taxonomy), Lois Blaine (ATCC), and Scott Federhen (NCBI). Many of these attendees went on to serve as curators for different branches of the classification. In particular, David Hillis, John Taylor, and Gary Olsen put in long hours to help the project move along.
In 1995, as more demands were made on the Taxonomy database,
the system was moved to a SyBase relational database
(
In 1997, the
Organismal taxonomy is a powerful organizing principle in the
study of biological systems. Inheritance, homology by common descent,
and the conservation of sequence and structure in the determination
of function are all central ideas in biology that are directly related
to the evolutionary history of any group of organisms. Because of this,
taxonomy plays an important cross-linking role in many of the
The NCBI Taxonomy database is a curated set of names and classifications
for all of the organisms that are represented in
Of the several different ways to build a taxonomy, our group maintains
a If two organisms (A and B) are listed more closely together in the taxonomy
than either is to organism C, the assertion is that C diverged from the
lineage leading to A+B earlier in evolutionary history, and that A and B
share a common ancestor that is not in the direct line of evolutionary
descent to species C. For example, the current consensus it that the closest
living relatives of the birds are the crocodiles; therefore, our classification
does not include the familiar taxon Reptilia (turtles, lizards and snakes,
and crocodiles), which excludes the birds, and would break the phylogenetic
principle outlined above.
Our classification represents an assimilation of information from many
different sources (see
We do not rely on sequence data alone to build our classification, and we do not perform phylogenetic analysis ourselves as part of the taxonomy project. Most of the organisms in GenBank are represented by only a snippet of sequence; therefore, sequence information alone is not enough to build a robust phylogeny. The vast majority of species are not there at all, although about 50% of the birds and the mammals are represented. We therefore also rely on analyses from morphological studies; the challenge of modern systematics is to unify molecular and morphological data to elucidate the evolutionary history of life on earth.
Currently, more than 100 new species are added to the database daily, and the rate is accelerating as sequence analysis becomes an ever more common component of systematic research and the taxonomic description of new species.
The
The number and complexity of organisms in a submission can vary enormously. Many contain a single new name, others may include 100 species, all from the same familiar genus, whereas others may include 100 names (only half identified at the species level) from 100 genera (all of which are new to the Taxonomy database) without any other identifying information at all.
Some new organism names are found by software when the protein
sequence databases (
We often receive consults on submissions with explicitly new species
names that will be published as part of the description of a new species.
These sequence entries (like any other) may be designated “hold
until published” (
Occasionally, the same new genus name is proposed simultaneously for different taxa; in one case, two papers with conflicting new names had been submitted to the same journal, and both had gone through one round of review and revision without detection of the duplication. Although these duplications would have been discovered in time, the increasingly common practice of including some sequence analysis in the description of a new species can lead to earlier detection of these problems. In many cases, the new species name proposed in the submitted manuscript is changed during the editorial review process, and a different name appears in the publication. Submitters are encouraged to inform us when their new descriptions have been published, particularly if the proposed names have been changed.
We strongly encourage the submission of strain names for cultured bacteria, algae, and fungi and for sequences from laboratory animals in biochemical and genetic studies; of cultivar names for sequences from cultivated plants; and of specimen vouchers (something that definitively ties the sequence to its source) for sequences from phylogenetic studies. There are many other kinds of useful information that may be contained within the sequence submission, but these data are the bare minimum necessary to maintain a reliable link between an entry in the sequence database and the biological source material.
The
TaxBrowser is updated continuously. New species will appear on a daily basis as the new names appear in sequence entries indexed during the daily release cycle of the Entrez databases. New taxa in the classification appear in TaxBrowser on an ongoing basis, as sections of the taxonomy already linked to public sequence entries are revised.
The browser produces two different kinds of Web pages:
hierarchy pages, which present a familiar indented taxon-specific pages, which summarize all of the information that
we associate with any particular taxonomic entry in the database. For
example, “hominidae” as a search term from the (
The taxon-specific browser display page shows all of the information
that is associated with a particular taxon in the Taxonomy database and
some information collected through links with related databases
( The name, taxid, rank,
There are two sets of links to Entrez records from the Taxonomy
Browser. The “subtree links” are accumulated up the tree
in a hierarchical fashion; for example, there are 16 million nucleotide
records and a half million protein records associated with the Chordata
(
“Direct links” will retrieve Entrez records that are
linked directly to this particular node in the taxonomy database. Many
of the Entrez domains (e.g., sequences and structures) are linked into
the taxonomy at or below the species level; it is a data error when a
sequence entry is directly linked into the taxonomy at a taxon somewhere
above the species level. For other Entrez domains (e.g., literature and
phylogenetic sets), this is not the case. A journal article may talk
about several different species but may also refer directly to the
The taxon-specific browser pages now also show the NCBI LinkOut links
to external resources. These include links to a broad range of different
kinds of resources and are provided for the convenience of our users; the
NCBI does not vouch for the content of these resources, although we do
make an effort to ensure that they are of good scientific quality. A
complete list of external resources can be found
There are several different ways to search for names in the Taxonomy database. If the search results in a terminal node in our taxonomy, the taxon-specific browser page is displayed; if the search returns with an internal (non-terminal) node, the hierarchical classification page is displayed.
Names can be duplicated in the Taxonomy database, but the taxonomy
browser can only be focused on a single taxon at any one time. If a
complete name search retrieves more than one entry from the taxonomy,
an intermediate name selection screen appears ( Searches for
There is a
The NCBI Taxonomy database is stored as a SyBase relational database, called TAXON. The NCBI taxonomy group maintains the database with a customized software tool, the Taxonomy Editor. Each entry in the database is a “taxon”, also referred to as a “node” in the database. The “root node” (taxid1) is at the top of the hierarchy. The path from the root node to any other particular taxon in the database is called its “lineage”; the collection of all of the nodes beneath any particular taxon is called its “subtree”. Each node in the database may be associated with several names, of several different nametypes. For indexing and retrieval purposes, the nametypes are essentially equivalent.
The Taxonomy database is populated with species names that have appeared in a sequence record from one of the nucleotide or protein databases. If a name has ever appeared in a sequence record at any time (even if it is not found in the current version of the record), we try to keep it in the Taxonomy database for tracking purposes (as a synonym, a misspelling, or other nametype), unless there are good reasons for removing it completely (for example, if it might cause a future submission to map to the wrong place in the taxonomy).
File | Uncompresses to | Description |
---|---|---|
taxdump.tar.Z |
readme.txt | A terse description of the dmp files |
nodes.dmp | Structure of the database; lists each taxid with its parent taxid, rank, and other values associated with each node (genetic codes, etc.) | |
names.dmp | Lists all the names associated with each taxid | |
delnodes.dmp | Deleted taxid list | |
merged.dmp | Merged nodes file | |
division.dmp | GenBank division files | |
gencode.dmp | Genetic codes files | |
gc.prt | Print version of genetic codes | |
gi_taxid_nucl.dmp.gz | gi_taxid_nucl.dmp | A list of gi_taxid pairs for every live gi-identified sequence in the nucleotide sequence database |
gi_taxid_prot.dmp.gz | gi_taxid_prot.dmp | A list of gi_taxid pairs for every live gi-identified sequence in the protein sequence database |
gi_taxid_nucl_diff.dmp | gi_taxid_nucl_diff | List of differences between latest gi_taxid_nucl and previous listing |
gi_taxid_prot_diff.dmp | gi_taxid_prot_diff | List of differences between latest gi_taxid_prot and previous listing |
For non-UNIX users, the file taxdmp.zip includes the same (zip compressed) data.
Each taxon in the database has a unique identifier, its taxid.
Taxids are assigned sequentially. When a taxon is deleted, its taxid
disappears and is not reassigned (
There are many possible types of names that can be associated
with an organism taxid in TAXON. To track and display the names
correctly, the various names associated with a taxid are tagged
with a nametype, for example “scientific name”,
“synonym”, or “common name”. Each taxid
When sequences are submitted to GenBank, usually only a scientific
name is included; most other names are added by NCBI taxonomists at
the time of submission or later, when further information is discovered.
For a complete description of each nametype used in TAXON, see
Scientific names, the only required nametype for a taxid, can be
further qualified into different classes. Not all “scientific
names” that accompany sequence submissions are true Linnaean
Latin binomial names; if the taxon is not identified to the species
level, it is not possible to assign a binomial name to it. For
indexing and retrieval purposes, TAXON needs to know whether the
scientific name is a Latin binomial name, or otherwise. A full
listing of the classes of TAXON scientific names can be viewed in
The treatment of duplicated names was discussed briefly in the section on the Taxonomy browser. For our purposes, there are four main classes of duplicated scientific names: (1) real duplicate names, (2) structural duplicates, (3) polyphyletic genera, and (4) other duplicate names.
There are several main codes of nomenclature for living organisms:
the Zoological Code (International Code of Zoological Nomenclature,
ICZN; for animals), the Botanical Code (International Code of Botanical
Nomenclature, ICBN; for plants), the Bacteriological Code (International
Code of Nomenclature of Bacteria, ICNB; for prokaryotes), and the Viral
Code (International Code of Virus Classification and Nomenclature, ICVCN;
for viruses). Within each code, names are required to be unique. When
duplicate names are discovered within a code, one of them is changed
(generally, the newer duplicate name). However, the codes are complex,
and not all names are subject to these restrictions. For example,
There is no real effort to make the scientific names of taxa unique among Codes, and among the relatively small set of names represented in the NCBI taxonomy database (20,000 genera), there are approximately 200 duplicate names (or about 1%), mostly at the genus level.
Early in 2002, the first duplicate species name was recorded in the
Taxonomy database.
In the Zoological and Bacteriological Codes, the subgenus that
Includes the type species is required to have the same name as the genus.
This is a systematic source of duplicate names. For these duplicates,
we use the associated rank in the unique name, e.g.,
Certain genera, especially among the asexual forms of Ascomycota
and Basidiomycota, are polyphyletic, i.e., they do not share a common
ancestor. Pending taxonomic revisions that will transfer species assigned
to “form” genera such as
We list many duplicate names in other nametypes (apart from our preferred “scientific name” for each taxon). Most of these are included for retrieval purposes, common names or the names of familiar paraphyletic taxa that we have not included in our classification, e.g. Osteichthyes, Coelenterata, and reptiles.
Aside from names, there are several optional types of information
that may be associated with a taxid. These are (1) rank, such as
species, genus or family; (2) genetic code, for translating proteins;
(3) GenBank division; (4) literature citations; and (5) abbreviated
lineage, for display in GenBank flat files. For more details on these
data types, see
The TAXON database is a node within the Entrez integrated retrieval
system (
Taxonomy was the first Entrez database to have an internal
hierarchical structure. Because Entrez deals with unordered sets
of objects in a given domain, an alternative way to represent these
hierarchical relationships in Entrez was required (see the section
The main focus of the Entrez Taxonomy
The default Entrez search is case insensitive and can be for any of
the names that can be found in the Taxonomy database. Thus, any of the
following search terms, Homo sapiens, homo sapiens, human, or Man, will
retrieve the node for
As for other Entrez databases, Taxonomy supports Boolean searching,
a
Each search result, listed in document summary (DocSum) format, may
have several links associated with it. For example, for the search
result Homo sapiens, the
A helpful list follows:
A search for Hominidae retrieves a single, hyperlinked entry.
Selecting the link shows the structure of the taxon. On the other
hand, a search for Hominidae[subtree] will retrieve a
nonhierarchical list of all of the taxa listed within the
Hominidae. A search for species[rank] yields a list of all species in
the Taxonomy database (108,020 in May 2002). Find the Taxonomy update frequency by selecting Entrez
An overview of the distribution of taxa in the DocSum list can be
seen if To filter out less interesting names from a DocSum list, add some
terms to the query, e.g., 2002/01/10[date] NOT uncultured[prop]
NOT unspecified[prop].
There are a variety of choices regarding how search results can be displayed in Taxonomy Entrez.
The Common Tree view shows an abbreviated view of the taxonomic
hierarchy and is designed to highlight the relationships between a
selected set of organisms. The ten species shown in
If there are more than few dozen taxa selected for the common
tree view, the display becomes visually complex and generally less
useful. When a large list of taxa is sent to the Common Tree display,
a summary screen is displayed first. For example, we currently list
727 families in the Viridiplantae (plants and green algae)
( The taxa are aggregated at the predetermined set of nodes in the
Taxonomy database that have been assigned “BLAST names”.
This serves an informal, very abbreviated, vernacular classification
that gives a convenient overview. The BLAST names will often not
provide complete coverage for all species at all levels in the tree.
Here, not all of our
There are several formatting options for saving the common tree display to a text file: text tree, phylip tree, and taxid list.
Hyperlinks to a common tree display can be made in two ways:
by specifying the common tree view in an Entrez query
by providing a list of taxids directly to the common tree
cgi function (for example,
The
As for any Entrez database, the contents are indexed by creating
term lists for each field of each database record (or taxid). For
There are five different index fields for names in Taxonomy Entrez.
The [lineage] and [subtree] index fields are a way to superimpose
the hierarchical relationships represented in the taxonomy on top of
the Entrez data model. For an example of how to use these field
limits for searching Taxonomy Entrez, see
The genetic code [gc], mitochondrial genetic code [mgc], and GenBank division [division] fields are all inherited within the taxonomy. The information in these fields refers to the genetic code used by a taxon or in which GenBank division it resides. Because whole families or branches may use the same code or reside in the same GenBank division, this property is usually indexed with a taxon high in the taxonomic tree, and the information is inherited by all those taxa below it. If there is no [gc] field associated with a taxon in the database, it is assumed that the standard genetic code is used. A genetic code may be referred to by either name or translation table number. For example, the two equivalent queries, standard[gc] and translation table 1[gc], each retrieves the set of organisms that use the standard genetic code for translating genomic sequences. Likewise, these two queries echinoderm mitochondrial[mgc] and translation table 9[mgc] will each retrieve the set of organisms that use the echinoderm mitochondrial genetic code for translating their mitochondrial sequences.
There are several useful terms and phrases indexed in the [prop] field. Possible search strategies that specify the prop field are explained below.
unspecified [prop] not identified at the species
level uncultured [prop] environmental sample
sequences unclassified [prop] listed in an “unclassified”
bin incertae sedis [prop] listed in an “incertae
sedis” bin
We do not explicitly flag names as “unspecified” in
All of these search strategies below are valid. Taxonomy
Eentrez displays only taxa that are linked to public sequence entries,
and because sequence entries are supposed to correspond to the Taxonomy
database at or below the species level, the Entrez query: terminal
[prop] NOT “at or below species level” [prop] should only
retrieve problem cases.
above genus level [prop] above species level [prop] “at or below species level” [prop] (needs
explicit quotes) below species level [prop] terminal [prop] non terminal [prop]
genetic code [prop] mitochondrial genetic code [prop] standard [prop] invertebrate mitochondrial
[prop] translation table 5 [prop] The query “genetic code [prop]”
retrieves all of the taxa at which one of the genomic genetic
codes is explicitly set. The second query retrieves all of the
taxa at which one of the mitochondrial genetic codes is explicitly
set, and so on. division [prop] INV [prop] invertebrates [prop]
The above terms index the assignments of the GenBank division
codes, which are divided along crude taxonomic categories (see
The remaining index fields are common to most or all Entrez domains, although some have special features in the taxonomy domain. For example, the field text word, [word], indexes words from the Taxonomy Entrez name indexes. Most punctuation is ignored, and the index is searched one word at a time; therefore, the search “homo sapiens[word]” will retrieve nothing.
Several useful terms are indexed in the properties field, [prop],
including functional nametypes and classifications, the rank level of
a taxon, and inherited values. See
More information on using the generic Entrez fields can be found
in the
Many of the Entrez databases (Nucleotide, Protein, Genome, etc.)
include an
To not retrieve such “exploded” terms, the unexploded
indexes should be used. This query will only retrieve the entries that
are linked directly to
Taxids are indexed with the prefix txid: txid9606 [orgn].
Source organism modifiers are indexed in the [properties] field, and such queries would be in the form: src strain[prop], src variety[prop], or src specimen voucher[prop]. These queries will retrieve all entries with a strain qualifier, a variety qualifier, or a specimen_voucher qualifier, respectively.
All of the organism source feature modifiers (/clone, /serovar, /variety, etc.) are indexed in the text word field, [text word]. For example, one could query GenBank for: “strain k-12” [text word]. Because strain information is inconsistent in the sequence databases (as in the literature), a better query would be: “strain k 12”[word] OR “strain k12”[word]. Note: explicit double-quotes may be necessary for some of these queries.
The Taxonomy
The checkboxes
Selecting one of the
A complete copy of the public NCBI taxonomy database is deposited
several times a day on our
Taxonomy BLAST reports (
The function library for the taxonomy application software in the
NCBI Toolkit is ncbitxc2.a (or libncbitxc2.a). The source code can be
found in the
In the early years of the project, Scott Federhen did all of the software and database development. In recent years, Vladimir Soussov and his group have been responsible for software and database development.
Scott Federhen (1990–present)
Andrzej Elzanowski (1994–1997)
Detlef Leipe (1994–present)
Mark Hershkovitz (1996–1997)
Carol Hotton (1997–present)
Mimi Harrington (1999–2000)
Ian Harrison (1999–2002)
Sean Turner (2000–present)
Rick Sternberg (2001–present)
If you have a comment or correction to our Taxonomy database,
perhaps a misspelling or classification or if something looks wrong,
please send a message to
Every node in the database is required to have exactly one
“scientific name”. Wherever possible, this is a
validly published name with respect to the relevant code of
nomenclature. Formal names that are subject to a code of
nomenclature and are associated with a validly published
description of the taxon will be Latinized uninomials above
the species level, binomials (e.g.
The scientific name is the one that will be used in all of
the sequence entries that map to this node in the Taxonomy database.
Entries that are submitted with any of the other names associated
with this node will be replaced with this name. When we change
the scientific name of a node in the Taxonomy database, the
corresponding entries in the sequence databases will be updated
to reflect the change. For example, we list
The “synonym” nametype is applied to both synonyms
in the formal nomenclatural sense (objective, nomenclatural,
homotypic
The “acronym” nametype is used primarily for the
viruses. The International Committee on Taxonomy of Viruses
(
The term “anamorph” is reserved for names applied
to asexual forms of fungi, which present some special nomenclatural
challenges. Many fungi are known to undergo both sexual and asexual
reproduction at different points in their life cycle (so-called
“perfect” fungi); for many others, however, only the
asexually reproducing (anamorphic or mitosporic) form is known (in
some, perhaps many, asexual species, the sexual cycle may have been
lost altogether). These anamorphs, often with simple and not especially
diagnostic morphology, were given Linnaean binomial names. A number of
named anamorphic species have subsequently been found to be associated
with sexual forms (teleomorphs) with a different name (for example,
The “misspelling” nametype is for simple misspellings. Some of these are included because the misspelling is present in the literature, but most of them are there because they were once found in a sequence entry (which has since been corrected). We keep them in the database for tracking purposes, because copies of the original sequence entry can still be retrieved. Misspellings are not listed on the TaxBrowser pages nor on the Taxonomy Entrez Info display views, but they are indexed in the Entrez search fields (so that searches and Entrez queries with the misspelling will find the appropriate node).
“Misnomer” is a rarely used nametype. It is used for names that might otherwise be listed as “misspellings” but which we want to appear on the browser and Entrez display pages.
The “common name” nametype is used for vernacular names associated with a particular taxon. These may be found at any level in the hierarchy; for example, “human”, “reptiles”, and “pale devil's-claw” are all used. Common names should be in lowercase letters, except where part of the name is derived from a proper noun, for example, “American butterfish” and “Robert's arboreal rice rat”.
The use of common names is inherently variable, regional, and often
inconsistent. There is generally no authoritative reference that
regulates the use of common names, and there is often not perfect
correspondence between common names and formally described scientific
taxa; therefore, there are some caveats to their use. For scientific
discourse, there is no substitute for formal scientific names.
Nevertheless, common names are invaluable for many indexing, retrieval,
and display purposes. The combination “
The “
The “in-part” nametype is included for retrieval
terms that have a broader range of application than the taxon or
taxa at which they appear. For example, we list reptiles and Reptilia
as in-part nametypes at our nodes
The “includes” nametype is the opposite of the in-part
nametype and is included for retrieval terms that have a narrower
scope of application than the taxon at which they appear. For example,
we could list “reptiles” as an “includes”
nametype for the
The “equivalent name” nametype is a catch-all category, used for names that we would like to associate with a particular node in the database (for indexing or tracking purposes) but which do not seem to fit well into any of the other existing nametypes.
The “genbank common name” was introduced to provide a mechanism by which, when there is more than one common name associated with a particular node in the taxonomy, one of them could be designated to be the common name that should be used by default in the GenBank flatfiles and other applications that are trying to find a common name to use for display (or other) purposes. This is not intended to confer any special status or blessing on this particular common name over any of the other common names that might be associated with the same node, and we have developed mechanisms to override this choice for a common name on a case-by-case basis if another name is more appropriate or desirable for a particular sequence entry. Each node may have at most one “genbank common name”.
There may be more than one acronym associated with a particular node in the Taxonomy database (particularly if several virus names have been synonymized in a single species). Just as with the “genbank common name”, the “genbank acronym” provides a mechanism to designate one of them to be the acronym that should be used for display (or other) purposes. Each node may have at most one “genbank acronym”.
The “genbank synonym” nametype is intended for those
special cases in which there is more than one name commonly used in
the literature for a particular species, and it is informative to have
both names displayed prominently in the corresponding sequence record.
Each node may have at most one “genbank synonym”. For example,
Although the use of either the anamorph or teleomorph name is
formally correct under the International Code of Botanical Nomenclature,
we prefer to give precedence to the telemorphic name as the
“scientific name” in the Taxonomy database, both to
emphasize their commonality and to avoid having two (or more) taxids
that effectively apply to the same organism. However, in many cases,
the anamorphic name is much more commonly used in the literature,
especially when sequences are normally derived from the asexual form
of the species. In these cases, the “genbank anamorph”
nametype can be used to annotate the corresponding sequence records
with both names. Each node may have at most one “genbank
anamorph”. For example:
Whenever possible, formal scientific names are used for taxa.
There are several codes of nomenclature that regulate the description
and use of names in different branches of the tree of life. These are:
the International Code of Zoological Nomenclature (
The viral code is less well developed than the others, but it includes
an official classification for the viruses as well as a list of approved
species names. Viral names are not Latin binomials (as required by the
other codes), although there are some instances (e.g.,
The zoological, botanical, and bacteriological codes mandate Latin
binomials for species names. They do not describe an official
classification (such as the
The fungi are subject to the botanical code. The cyanobacteria (blue-green algae) have been subject to both the botanical and the bacteriological codes, and the issue is still controversial.
“Authorities” appear at the end of the formal species
name and include at least the name or standard abbreviation of the
taxonomist who first described that name in the scientific literature.
Other information may appear in the authority as well, often the year
of description, and can become quite complicated if the taxon has been
transferred or amended by other taxonomists over the years. We do not
use authorities in our taxon names, although many are included in the
database listed as synonyms. We have made an exception to this rule in
the case of our first duplicated species name in the database,
All three of the codes of nomenclature for cellular organisms
provide for names at the subspecies level. The botanical and
bacteriological codes include the string “subsp.” in the
formal name; the zoological code does not, e.g.,
The botanical code (but none of the others) provides for two
additional formal ranks beneath the subspecies level, varietas and
forma. These names will include the strings “var.” and
“f.”, respectively, e.g.,
We list taxa with other subspecific names where it seems useful
and appropriate and where it is necessary to find places for names
in the sequence databases. For indexing purposes in the Genomes
division of Entrez, it is convenient to have strain-level nodes for
bacterial species with a complete genome sequence, particularly when
there are two or more complete genome sequences available for
different strains of the same species, e.g.,
Several other classes of subspecific groups do not have formal
standing in the nomenclature but represent well-characterized and
biologically meaningful groups, e.g., serovar, pathovar, forma
specialis, and others. In many cases, these may eventually be promoted
to a species; therefore, it is convenient to represent them
independently from the outset, e.g.,
Many other names below the species level have been added to the Taxonomy database to accommodate SWISS-PROT entries, where strain (and other) information is annotated with the organism name for some species.
In general, we try to avoid unqualified species names such as
When entries are not identified at the species level, multiple
sequences can be from the same unidentified species. Sequences
from multiple different unidentified species in the same genus
are also possible. To keep track of this, we add unique informal
names to the Taxonomy database, e.g., a meaningful identifier
from the submitters could be used. This could be a strain name,
a culture collection accession, a voucher specimen, an isolate
name or location—anything that could tie the entry to the
literature (or even to the lab notebook). If nothing else is
available, we may construct a unique name using a default formula
such as the submitter's initials and year of submission. This way,
if a formal name is ever determined or described for any of these
organisms, we can synonymize the informal name with the formal
one in the Taxonomy database, and the corresponding entries in
the sequence databases will be updated automatically. For example,
AJ302786 was originally submitted (in November 2000) as
Here are some examples of informal names in the Taxonomy database:
We use single quotes when it seems appropriate to group a phrase into a single lexical unit. Some of these names include abbreviations with special meanings.
“n. sp.” indicates that this is a new, undescribed species and not simply an unidentified species. “sp. nr.” indicates “species near”. In the example above, this indicates that this is similar to Camponotus gasseri. “aff.”, affinis, related to but not identical to the species given. “cf.”, confer; literally, “compare with” conveys resemblance to a given species but is not necessarily related to it. “s.l.”, sensu lato; literally, “in the broad sense”. “ex”, “from” or “out of” the biological host of the specimen.
Note that names with cf., aff., nr., and n. sp. are not unique and should have unique identifiers appended to the name.
Cultured bacterial strains and other specimens that have not been identified to the genus level are given informal names as well, e.g., Desulfurococcaceae str. SRI-465; crenarchaeote OlA-6.
Names such as Camponotus sp. 1 are avoided, because different
submitters might easily use the same name to refer to different species.
See
Sequences from environmental samples are given “uncultured” names. In these studies, nucleotide sequences are cloned directly from the environment and come from varied sources, such as Antarctic sea ice, activated sewer sludge, and dental plaque. Apart from the sequence itself, there is no way to identify the source organisms or to recover them for further studies. These studies are particularly important in bacterial systematics work, which shows that the vast majority of environmental bacteria are not closely related to laboratory cultured strains (as measured by 16S rRNA sequences). Many of the deepest-branching groups in our bacterial classification are defined only by anonymous sequences from these environmental samples studies, e.g., candidate division OP5, candidate division Termite group 1, candidate subdivision kps59rc, phosphorous removal reactor sludge group, and marine archael group 1.
These samples vary widely in length and in quality, from short
single-read sequences of a few hundred base pairs to high-quality,
full-length 16S sequences. We now give all of these samples anonymous
names, which may indicate the phylogenetic affiliation of the sequence,
as far is it may be determined, e.g., uncultured archaeon, uncultured
crenarchaeote, uncultured gamma proteobacerium, or uncultured enterobacterium.
See
Some groups of bacteria have never been cultured but can be characterized and reliably recovered from the environment by other means. These include endosymbiotic bacteria and organisms similar to the phytoplasmas, which can be identified by the plant diseases that they cause. We do not give these “uncultured” names, as above. These represent a special challenge for bacterial nomenclature, because a formal species description requires the designation of a cultured type strain. The bacteriological code has a special provision for names of this sort, Candidatus, e.g., Candidatus Endobugula or Candidatus Endobugula sertula; Candidatus Phlomobacter or Candidatus Phlomobacter fragariae. These often appear in the literature without the Candidatus prefix; therefore, we list the unqualified names as synonyms for retrieval purposes.
We allow informal names for unranked nodes above the species level as well. These should all be phylogenetically meaningful groups, e.g., the Fungi/Metazoa group, eudicotyledons, Erythrobasidium clade, RTA clade, and core jakobids. In addition, there are several other classes of nodes and names above the species level that explicitly do not represent phylogenetically meaningful groups. These are outlined below.
We are expected to add new species names to the database in a timely manner, preferably within a day or two. If we are able to find only a partial classification for a new taxon in the database, we place it as deeply as we can and list it in an explicit “unclassified” bin. As more information becomes available, these bins are emptied, and we give full classifications to the taxa listed there. In general, we suppress the names of the unclassified bins themselves so they do not appear in the abbreviated lineages that appear in the GenBank flatfiles, e.g., unclassified Salticidae, unclassified Bacteria, and unclassified Myxozoa.
If the best taxonomic opinion available is that the position of
a particular taxon is uncertain, then we will list it in an
“incertae sedis” bin. This is a more permanent assignment
than for taxa that are listed in unclassified bins, e.g.,
Fungi that were known only in the asexual (mitosporic, anamorphic)
state were placed formerly in a separate, highly polyphyletic category
of “imperfect” fungi, the Deuteromycota. Spurred especially
by the development of molecular phylogenetics, current mycological
practice is to classify anamorphic species as close to their sexual
relatives as available information will support. Mitosporic categories
can occur at any rank, e.g.,
The requirement that the Taxonomy database includes names from all of the entries in the sequence database introduces a number of names that are not typically treated in a taxonomic database. These are listed in the top-level group “Other”. Plasmids are typically annotated with their host organism, using the /plasmid source organism qualifier. Broad-host-range plasmids that are not associated with any single species are listed in their own bin. Plasmid and transposon names from very old sequence entries are listed in separate bins here as well. Plasmids that have been artificially engineered are listed in the “vectors” bin.
We do not require that Linnaean ranks be assigned to all of our taxa, but we do include a standard rank table that allows us to assign formal ranks where it seems appropriate. We do not require that sibling taxa all have the same rank, but we do not allow taxa of higher rank to be listed beneath taxa of lower rank. We allow unranked nodes to be placed at any point in our classification.
The one rank that we particularly care about is “species”. We try to ensure that all of the sequence entries map into the Taxonomy database at or below a species-level node.
The genetic codes and mitochondrial genetic codes that are
appropriate for translating protein sequences in different branches
of the tree of life are assigned at nodes in the Taxonomy database
and inherited by species at the terminal branches of the tree. Plastid
sequences are all translated with the standard genetic code, but many
of the mRNAs undergo extensive RNA editing, making it difficult or
impossible to translate sequences from the plastid genome directly.
The genetic codes are listed on our
GenBank taxonomic division assignments are made in the Taxonomy database and inherited by species at the terminal branches of the tree, just as with the genetic codes.
The Taxonomy database allows us to store comments and references
at any taxon. These may include hotlinks to abstracts in
Some branches of our taxonomy are many levels deep, e.g., the bony fish (as we moved to a phylogenetic classification) and the drosophilids (a model taxon for evolutionary studies). In many cases, the classification lines in the GenBank flatfiles became longer than the sequences themselves. This became a storage and update issue, and the classification lines themselves became less helpful as generally familiar taxa names became buried within less recognizable taxa.
To address this problem, the Taxonomy database allows us to flag taxa that should (or should not) appear in the abbreviated classification line in the GenBank flatfiles. The full lineages are indexed in Entrez and displayed in the Taxonomy Browser.
Three-dimensional.
An Accession number is a unique identifier given to a sequence when it is submitted to one of the DNA repositories (GenBank, EMBL, DDBJ). The initial deposition of a sequence record is referred to as version 1. If the sequence is updated, the version number is incremented, but the Accession number will remain constant.
The
One of the variant forms of a gene at a particular
Application Programming Interface. An API is a set of routines that an application uses to request and carry out lower-level services performed by a computer's operating system. For computers running a graphical user interface, an API manages an application's windows, icons, menus, and dialog boxes.
Abstract Syntax Notation 1 is an international standard data-representation format used to achieve interoperability between computer platforms. It allows for the reliable exchange of data in terms of structure and content by computer and software systems of all types.
Bacterial Artificial Chromosome. A BAC is a large segment of DNA (100,000–200,000 bp) from another species cloned into bacteria. Once the foreign DNA has been cloned into the host bacteria, many copies of it can be made.
BankIt is a tool for the online submission of one or a few sequences
into
The value S′ is derived from the raw alignment score S in which
the statistical properties of the scoring system used have been taken into
account. By normalizing a raw score using the formula:
Basic Local Alignment Search Tool (
nucleotide–nucleotide BLAST. blastn takes nucleotide sequences in
protein–protein BLAST. blastp takes protein sequences in
A DNA/Protein sequence analysis program to quickly find sequences of
95% and greater similarity of length 40 bases or more. It may miss
more divergent or shorter sequence alignments. BLAT on proteins finds sequences
of 80% and greater similarity of length 20 amino acids or more.
BLAT is not BLAST. (See the
BLAST Link. BLink displays the results of
Binary Large Object (or binary data object). BLOB refers to a large piece of data, such as a bitmap. A BLOB is characterized by large field values, an unpredictable table size, and data that are formless from the perspective of a program. It is also a keyword designating the BLOB structure, which contains information about a block of data.
Blocks Substitution Matrix. A substitution matrix in which scores for each
position are derived from observations of the frequencies of substitutions in
blocks of local alignments in related proteins. Each matrix is tailored to a
particular evolutionary distance. In the
This term refers to binary algebra that uses the logical operators AND, OR, XOR, and NOT; the outcomes consist of logical values (either TRUE or FALSE). The keyword boolean indicates that the expression or constant expression associated with the identifier takes the value TRUE or FALSE. The logical-AND (&&) operator produces the value 1 if both operands have nonzero values; otherwise, it produces the value 0. The logical-OR (×€×€) operator produces the value 1 if either of its operands has a nonzero value. The logical-NOT (!) operator produces the value 0 if its operand is true (nonzero) and the value 1 if its operand is FALSE (0). The exclusive OR (XOR) operator yields TRUE only if one of its operands are TRUE and the other is FALSE. If both operands are the same (either TRUE or FALSE), the operation yields FALSE.
A run of the genome assembly and annotation process of the set of products generated by that run.
Cancer Chromosome Aberration Project. CCAP was designed to expedite the
definition and detailed characterization of the distinct chromosomal alterations
that are associated with malignant transformation. The project is a collaboration
among the
Conserved Domain. CD refers to a domain (a distinct functional and/or structural unit of a protein) that has been conserved during evolution. During evolution, changes at specific positions of an amino acid sequence in the protein have occurred in a way that preserve the physico-chemical properties of the original residues, and hence the structural and/or functional properties of that region of the protein.
Conserved Domain Architecture Retrieval Tool. When given a protein query
sequence, CDART displays the functional domains that make up the protein and
lists proteins with similar domain architectures. The functional domains for
a sequence are found by comparing the protein sequence to a database of conserved
domain alignments,
Conserved Domain Database. This database is a collection of sequence alignments and profiles representing protein domains conserved during molecular evolution.
complementary DNA. A
coding region, coding sequence. CDS refers to the portion of a genomic DNA sequence that is translated, from the start codon to the stop codon, inclusively, if complete. A partial CDS lacks part of the complete CDS (it may lack either or both the start and stop codons). Successful translation of a CDS results in the synthesis of a protein.
Cancer Genome Anatomy Project. CGAP is an interdisciplinary program to
identify the human genes expressed in different cancerous states, based on
cDNA (
Comparative Genomic Hybidization. CGH is a fluorescent molecular cytogenetic
technique that identifies chromosomal aberrations and maps these changes to
metaphase chromosomes. CGH can be used to generate a map of DNA copy number
changes in tumor genomes. CGH is based on quantitative two-color fluorescence
Common Gateway Interface. A mechanism that allows a Web server to run a program or script on the server and send the output to a Web browser.
A group that is created based on certain criteria. For example, a gene cluster may include a set of genes whose similar expression profiles are found to be similar according to certain criteria, or a cluster may refer to a group of clones that are related to each other by homology.
“See in 3-D” is a structure and sequence alignment viewer
for NCBI databases. It allows viewing of 3-D structures and sequence–structure
or structure–structure alignments. Cn3D can work as a helper application
to the browser or as a client–server application that retrieves
structure records from the Molecular Modeling Database (MMDB, see below)
directly from the internet. The
Sequence of three nucleotides in DNA or mRNA that specifies a particular amino acid during protein synthesis; also called a triplet. Of the 64 possible codons, 3 are stop codons, which do not specify amino acids.
Clusters of Orthologous Groups (of proteins) were delineated by comparing protein sequences from completely sequenced genomes. Each COG consists of individual proteins or groups of paralogs from at least three lineages and thus corresponds to an ancient conserved domain.
The nucleotides or amino acids found most commonly at each position in the sequences of homologous DNAs, RNAs, or proteins.
A contiguous segment of the genome made by joining overlapping clones or sequences. A clone contig consists of a group of cloned (copied) pieces of DNA representing overlapping regions of a particular chromosome. A sequence contig is an extended sequence created by merging primary sequences that overlap. A contig map shows the regions of a chromosome where contiguous DNA segments overlap. Contig maps provide the ability to study a complete and often large segment of the genome by examining a series of overlapping clones, which then provide an unbroken succession of information about that region.
Central Processing Unit. The CPU is the computational and control unit of a computer, the device that interprets and executes instructions.
Cascading Style Sheets. CSS specify the formatting details that control
the presentation and layout of
A tool of
Data Creation and Maintenance System
A sequence in FASTA format begins with a single-line description,
followed by lines of sequence data. The definition line or description line
is distinguished from the sequence data by a “greater than”
(>) symbol in the first column (see
Deoxyribonucleic acid is the chemical inside the nucleus of a cell that carries the genetic instructions for making living organisms. DNA is composed of two anti-parallel strands, each a linear polymer of nucleotides. Each nucleotide has a phosphate group linked by a phosphoester bond to a pentose (a five-carbon sugar molecule, deoxyribose), that in turn is linked to one of four organic bases, adenine, guanine, cytosine, or thymine, abbreviated A, G, C, and T, respectively. The bases are of two types: purines, which have two rings and are slightly larger (A and G); and pyrimidines, which have only one ring (C and T). Each nucleotide is joined to the next nucleotide in the chain by a covalent phosphodiester bond between the 5′ carbon of one deoxyribose group and the 3′ carbon of the next. DNA is a helical molecule with the sugar–phosphate backbone on the outside and the nucleotides extending toward the central axis. There is specific base-pairing between the bases on opposite strands in such a way that A always pairs with T and G always pairs with C.
A “domain” refers to a discrete portion of a protein assumed to fold independently of the rest of the protein and which possesses its own function.
Draft sequence refers to DNA sequence that is not yet finished but
is generally of high quality (i.e., an accuracy of greater than 90%).
Draft sequence data are mostly in the form of 10,000 base pair-sized fragments,
the approximate chromosomal locations of which are known. The following keywords
are associated with draft sequence: phase 0, light-pass coverage of a clone,
generally only 1× coverage; phase 1, 4–10×
coverage of a
Document Type Definition. The DTD is an optional part of the prolog of an XML document that defines the rules of the document. It sets constraints for an XML document by specifying which elements are present in the document and the relationships between elements, e.g., which tags can contain other tags, the number and sequence of the tags, and attributes of the tags. The DTD helps to validate the data when the receiving application does not have a built-in description of the incoming data.
A program for filtering low-complexity regions from nucleic acid sequences.
Expect value. The E-value is a parameter that describes the number of
hits one can “expect” to see by chance when searching a
database of a particular size. It decreases exponentially with the score
(S) that is assigned to a match between two sequences. Essentially, the
E-value describes the random background noise that exists for matches
between sequences. For example, an E-value of 1 assigned to a hit can be
interpreted as meaning that in a database of the current size, one might
expect to see one match with a similar score simply by chance. This means
that the lower the E-value, or the closer it is to “0”,
the higher is the “significance” of the match. However, it
is important to note that searches with short sequences can be virtually
identical and have relatively high E-value. This is because the calculation
of the E-value also takes into account the length of the query sequence.
This is because shorter sequences have a high probability of occurring in
the database purely by chance. For more information, see the following
A number assigned to a type of enzyme according to a scheme of
standardized enzyme nomenclature developed by the Enzyme Commission of
the Nomenclature Committee of the International Union of Biochemistry and
Molecular Biology (IUBMB). EC numbers may be found in
Entrez is a retrieval system for searching several linked databases.
It provides access to the following NCBI databases:
Expressed Sequence Tag. ESTs are short (usually approximately 300–500
base pairs), single-pass sequence reads from
Electronic
“Ahead-of-print” citation.
Exon Finding by Sequence Homology. Exofish is a tool based on
homology searches for the rapid and reliable identification of human
genes. It relies on the sequence of another vertebrate, the pufferfish
Refers to the portion of a gene that encodes for a part of that gene's mRNA.
A gene may comprise many exons, some of which may include only protein-coding
sequence; however, an exon may also include 5' or 3' untranslated sequence.
Each exon codes for a specific portion of the complete protein. In some species
(including humans), a gene's exons are separated by long regions of DNA (called
Exon trapping is a technique for cloning exon sequences from genomic
DNA by selecting for functional splice sites, relying on the cellular splicing
machinery. The genomic DNA containing the putative exon(s) is cloned into
an exon-trap vector, which has a promoter, polyadenylation signals, and
splice sites, and then transfected into a cell line. If there are functional
splice sites in the genomic DNA fragment, the segments of DNA between the
splice sites will be removed. Total RNA is isolated and reverse-transcribed.
After
The first widely used algorithm for similarity searching of protein and
DNA sequence databases. The program looks for optimal local alignments by
scanning the sequence for small matches called “words”. Initially,
the scores of segments in which there are multiple word hits are calculated
(“init1”). Later, the scores of several segments may be summed
to generate an “initn” score. An optimized alignment that includes
gaps is shown in the output as “opt”. The sensitivity and speed
of the search are inversely related and controlled by the “k-tup”
variable, which specifies the size of a “word”
(
The pattern of bands on a gel produced by a clone when restricted by a
particular enzyme, such as
High-quality, low-error DNA sequence that is free of gaps. To qualify as a finished sequence, only a single error out of every 10,000 bases (i.e., an accuracy of 99.999%) is allowed.
Fluorescence
A flat file is a data file that contains records (each corresponding to a row in a table); however, these records have no structured relationships. To interpret these files, the format properties of the file should be known. For example, a database management system may allow the user to export data to a comma-delimited file. Such a file is called a flat file because it has no inherent information about the data, and interpretation requires additional information. Files in a database management system have more complex storage structures.
To copy changing data so as to preserve the dataset as it existed at a particular point in time. Also used to refer to the resulting set of frozen data.
File Transfer Protocol. A method of retrieving files over a network directly to the user's computer or to his/her home directory using a set of protocols that govern how the data are to be transported.
A gap is a space introduced into an alignment to compensate for insertions
and deletions in one sequence relative to another. To prevent the accumulation
of too many gaps in an alignment, introduction of a gap causes the deduction
of a fixed amount (the gap score) from the alignment score. Extension of the
gap to encompass additional nucleotides or amino acid is also penalized in the scoring
of an alignment. (See the
gigabytes
GenBank is a database of nucleotide sequences from more than 100,000
organisms. Records that are annotated with coding region features also include
amino acid translations. GenBank belongs to an international collaboration of
sequence databases that also includes
The instructions in a gene that tell the cell how to make a specific protein.
A, T, G, and C are the “letters” of the
A gene identification algorithm that is used to identify exon–intron structures in genomic DNA sequence.
The genetic identity of an individual that does not show as outward characteristics. The genotype refers to the pair of alleles for a given region of the genome that an individual carries.
Gene Expression Omnibus. GEO is a gene expression data repository and
online resource for the retrieval of gene expression data from any organism
or artificial source. Many types of gene expression data from platform types,
such as spotted microarray, high-density oligonucleotide array, hybridization
filter, and serial analysis of gene expression (
The GenInfo Identifier is a sequence identification number for a
nucleotide sequence. If a nucleotide sequence changes in any way, a new
GI number will be assigned. A separate GI number is also assigned to each
protein translation within a nucleotide sequence record, and a new GI is
assigned if the protein translation changes in any way. GI sequence identifiers
run parallel to the new accession.version system of sequence identifiers (see
the description of
Genome Survey Sequences are analogous to
The probability that a diploid individual will have two different alleles at a particular genome locus. These individuals are defined as heterozygous, whereas individuals who have two identical alleles at the locus are defined as homozygous. The probability can be estimated by sampling a representative number of individuals from the population and dividing the number of heterozygotes by the total number sampled.
Human Immunodeficiency Virus. HIV-1 is a retrovirus that is recognized as the causative agent of AIDS (Acquired Immunodeficiency Syndrome).
Hereditary nonpolyposis colon cancer
A region of the chromosome identified cytologically by DNA staining or
the
The term refers to similarity attributable to descent from a common ancestor. Homologous chromosomes are members of a pair of essentially identical chromosomes, each derived from one parent. They have the same or allelic genes with genetic loci arranged in the same order. Homologous chromosomes synapse during meiosis.
High-Throughput Genomic Sequences. The source of HTGS are large-scale genome
sequencing centers;
A keyword added to GenBank entries by sequencing centers to indicate that work has stopped on a clone and that the existing sequence will not be finished. Sequencing centers may stop work because the clone is redundant or for various other reasons.
Keywords added to GenBank entries by sequencing centers to indicate
the status (phase) of the sequence (see phase definitions described under
Hypertext Markup Language. HTML is derived from
Hold Until Published. HUP refers to the category for data that is electronically submitted for when it should be released to the public.
International Code of Botanical Nomenclature
International Classification of Diseases
International Code of Nomenclature of Bacteria
International Code of Nomenclature for Cultivated Plants
A diagrammatic representation of the karyotype of an organism.
Integrated Molecular Analysis of Genomes and their Expression. A consortium
of academic groups that share high-quality, arrayed cDNA libraries and
place sequence, map, and expression data of the clones in these arrays into
the public domain. With the use of this information, unique clones can be
rearrayed to form a “master array”, with the aim of ultimately
having a representative cDNA from every gene in the genome under study. To
date, human, mouse, rat, zebrafish, and
Refers to that portion of the DNA sequence that is present in the primary
transcript and that is removed by splicing during RNA processing and is not
included in the mature, functional
Indexed Sequential-Access Method. ISAM is a database access method. It allows data records in a database to be accessed either sequentially (in the order in which they were entered) or randomly (using an index). In the index, each record has a unique key that enables its rapid location. The key is the field used to reference the record.
International System for Human Cytogenetic Nomenclature
The particular chromosome complement of an individual or a related group of individuals, as defined by both the number and morphology of the chromosomes, usually in mitotic metaphase, and arranged by pairs according to the standard classification.
Laboratory Information Management Systems. LIMS comprise software that helps biological and chemical laboratories handle data generation, information management, and data archiving.
A registry service to create links from specific articles, journals, or
biological data in
In a genomic contect, locus refers to position on a chromosome. It may, therefore, refer to a marker, a gene, or any other landmark that can be described.
Each new
LocusLink provides a single query interface to curated sequence and
descriptive information about genetic loci. LocusLink issues a stable ID
(
Multiple Alignment Construction and Analysis Workbench. MACAW is a program for locating, analyzing, and editing blocks of localized sequence similarity among multiple seqences and linking them into a composite multiple alignment.
The Map Viewer is a software component of
megabytes
MEDLINE is
MegaBLAST is a program for aligning sequences that differ slightly as a result of
sequencing or other similar “errors”. When larger word size is used,
it is up to 10 times faster than more common sequence-similarity programs. MegaBLAST
is also able to efficiently handle much longer DNA sequences than the
Medical Subject Headings. MeSH refers to the controlled vocabulary of
Multi-FASTA format.
Mammalian Gene Collection.
Repetitive stretches of short sequences of DNA used as genetic markers to track inheritance in families (e.g., CC[TATATATA]CCCT). Also known as short tandem repeats (STRs).
Mendelian Inheritance in Man. First published in 1966,
An ordered list or map that defines the minimal set of overlapping clones
needed to provide complete coverage of a chromosome or other extended segment
of DNA (compare with
Molecular Modeling Database. MMDB is a database of three-dimensional biomolecular structures derived from X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy.
Molecular Modeling Database Accession number.
messenger RNA. mRNA describes the section of a genomic DNA sequence
that is transcribed, and can include the 5' untranslated region (5'UTR),
A permanent structural alteration in DNA. In most cases, DNA changes have either no effect or cause harm, but occasionally a mutation can improve an organism's chance of surviving, and the beneficial change is passed on to the organism's descendants. Typically, mutations are more rare than polymorphisms in population samples because natural selection recognizes their lower fitness and removes them from the population.
Contains supported software tools from the Information Engineering
Branch (IEB) of the NCBI. The NCBI Toolkit describes the three components
of the ToolBox: data model, data encoding, and programming libraries. Provides
access to documentation for the DataModel, C Toolkit, C++ Toolkit, NCBI
C Toolkit Source Browser, XML Demo Program, XML DTDs, and the
NEXUS refers to a file format designed to contain data for processing
by computer programs. NEXUS files should end with .nxs or .nex for purposes
of clarity (
Nuclear Magnetic Resonance. NMR is a spectroscopic technique used for the determination of protein structure.
non-redundant Protein Data Bank
Online Mendelian Inheritance in Man. OMIM is a directory of human genes and genetic disorders, with links to literature references, sequence records, maps, and related databases.
Orthology describes genes in different species that derive from a single ancestral gene in the last common ancestor of the respective species.
Orthology describes genes in different species that derive from a common ancestor, i.e., they are direct evolutionary counterparts.
A paralog is one of a set of homologous genes that have diverged from
each other as a consequence of gene duplication. For example, the mouse
α-
Paralogy describes the relationship of homologous genes that arose by gene duplication.
Polymerase Chain Reaction. A technique for amplifying a specific DNA segment in a complex mixture. Also present in the DNA mixture are short oligonucleotide primers to the DNA segment of interest and reagents for DNA synthesis. PCR relies on the ability of DNA to separate into its two complementary strands at high temperature (a process called denaturation) and for the two strands to anneal at an optimal lower temperature (annealing). The annealing phase is followed by a DNA synthesis step at an optimal temperature for a heat-stable DNA polymerase. After multiple rounds of denaturation, annealing, and DNA synthesis, the DNA sequence specified by the oligonucleotide primers is amplified.
The observable traits or characteristics of an organism, e.g., hair color, weight, or the presence or absence of a disease. Phenotypic traits are not necessarily genetic.
A computer program that assembles raw sequence into sequence contigs
(see above) and assigns to each position in the sequence an associated
“quality score”, on the basis of the
A computer program that analyses raw sequence to produce a “base
call” with an associated “quality score” for each position
in the sequence. A PHRED quality score of
Pattern of presence–absence of a cluster of orthologs (COG) in different species.
PubMed ID number
Portable Network Graphics. An extensible file format for the lossless,
well-compressed storage of raster images (images that are composed of horizontal
lines of pixels, such as those created by a computer screen). Compression of
image, media, and application files is necessary to reduce the transmission time
across the web. The technique of lossless compression reduces the size of the
file without sacrificing any original data, and the image after expansion is
exactly as it was before compression. PNG overcomes the patent issues of GIF
(Graphic Interchange Format) and can replace many common uses of TIFF (Tagged
Image File Format). Several features such as indexed color, grayscale, and
truecolor are supported, as well as an optional alpha-channel. PNG is designed
to work well in online viewing applications and is supported as an image standard
by the
A string of adenylic acid residues that are added to the 3′ end of
the primary
A common variation in the sequence of
Linear polymer of amino acids connected by peptide bonds. Proteins are large polypeptides, and the two terms are commonly used interchangeably.
Variations that are only common in specific populations. Usually such populations are reproductively isolated from other, larger groups. These variations may be completely absent in other groups.
A database of protein sequences from eight organisms: human (
A sequence of DNA that is very similar to a normal gene but that has been altered slightly so that it is not expressed. Such genes were probably once functional but, over time, acquired one or more mutations that rendered them incapable of producing a protein product.
Position-Specific Iterated BLAST. PSI-BLAST (
Position-Specific Score Matrix. The PSSM gives the log-odds score for finding a particular matching amino acid in a target sequence.
A retrieval system containing citations, abstracts, and indexing terms for
journal articles in the biomedical sciences. It includes literature citations
supplied directly to NCBI by publishers as well as
PubMed Central XML file
A queuing system to BLAST that allows users to retrieve their results at their convenience and format their results multiple times with different formatting options.
Quantitative Trait Locus. A QTL is a hypothesis that a certain region of the chromosome contains genes that contribute significantly to the expression of a complex trait. QTLs are generally identified by comparing the linkage of polymorphic molecular markers and phenotypic trait measurements. The density of the linkage map is important in the accurate and precise location of QTLs; the higher the map density, the more precise the location of the putative QTL, although there is increased likelihood that false positives will be detected. Once QTLs have been mapped to a relatively small chromosomal region, other molecular methods can be used to isolate specific genes.
Reciprocal best hits are proteins from different organisms that are each other's top BLAST hit, when the proteomes from those organisms are compared to each other. For example, proteins A–Z in organism 1 are compared against proteins AA–ZZ in organism 2. If protein A has a best hit to protein RR, and RR's best hit, when it is compared to all the proteins in organism 1, also turns out to protein A, then A and RR are reciprocal best hits. However, if RR's best hit is to B rather than to A, then A and RR are not reciprocal best hits.
RefSeq is the NCBI database of reference sequences; a curated, non-redundant set including genomic DNA contigs, mRNAs and proteins for known genes, and entire chromosomes.
Restriction Fragment Length Polymorphism. Genetic variations at the site where a restriction enzyme cuts a piece of DNA. Such variations affect the size of the resulting fragments. These sequences can be used as markers on physical maps and linkage maps. RFLP is also pronounced “rif lip”.
Radiation Hybrid map. A genome map in which
Ribonucleic Acid. A single-stranded nucleic acid, similar to
Reverse Position-Specific BLAST. A program used to identify conserved
domains in a protein query sequence. It does this by comparing a query
protein sequence to position-specific score matrices (
Serial Analysis of Gene Expression. An experimental technique designed to quantitatively measure gene expression.
Sequin is a stand-alone software tool developed by the
Saccharomyces Genome Database. A database for the molecular biology
and genetics of
Standard Generalized Markup Language. The international standard for
specifying the structure and content of electronic documents. SGML is used
for the markup of data in a way that is self-describing. SGML is not a language
but a way of defining languages that are developed along its general principles.
A subset of SGML called
Spectral Karyotyping. SKY is a technique that allows for the visualization
of all of an organism's chromosomes together, each labeled with a different
color. This is achieved by using chromosome-specific, single-stranded DNA
probes (each labeled with a different fluorophore) to hybridize or bind to
the chromosomes of a cell; resulting in each chromosome being painted a
different color. This technique is useful for identifying chromosome abnormalities
because it is easy to spot instances where a chromosome painted in one color
has a small piece of another chromosome, painted in a different color, attached
to it. (Also see
1. A software tool to automatically convert the short-form karyotype into an image representation of a cell or clone, with each chromosome displayed in a different color, with band overlay. The program will also incorporate the number of cells for each structural abnormality, which is displayed in brackets. 2. The full ideogram or a cell or clone, with each chromosome displayed in a different color, with band overlay.
Simple Modular Architecture Research Tool. A tool to allow automatic
identification and annotation of domains in user-supplied protein sequences.
For example, the
Common, but minute, variations that occur in human DNA at a frequency of 1 every 1,000 bases. An SNP is a single base-pair site within the genome at which more than one of the four possible base pairs is commonly found in natural populations. Several hundred thousand SNP sites are being identified and mapped on the sequence of the genome, providing the densest possible map of genetic differences. SNP is pronounced “snip”.
Simple Omnibus Format in Text. SOFT is an ASCII text format that was
designed to be a machine-readable representation of data retrieved from,
or submitted to, the Gene Expression Omnibus (
Refers to the location of the exon-intron junctions in a pre-mRNA (i.e.,
the primary transcript that must undergo additional processing to become
a mature RNA for translation into a protein). Splice sites can be
determined by comparing the sequence of genomic DNA with that of the
Sequence Search and Alignment by Hashing Algorithm. SSAHA is a software tool for very fast matching and alignment of DNA sequences and is used for searching databases containing large amounts (gigabases) of genome sequence. It achieves its fast search speed by converting sequence information into a “hash table” data structure, which can then be searched very rapidly for matches (Ning et al., Genome Res 11:1725-1729; 2001).
Simple Sequence Length Polymorphisms. SSLPs are markers based on the variation in the number of short tandem repeats in DNA.
A short DNA segment that occurs only once in the human genome, the exact location and order of bases of which are known. Because each is unique, STSs are helpful for chromosome placement of mapping and sequencing data from many different laboratories. STSs serve as landmarks on the physical map of the human genome.
A substitution matrix containing values proportional to the probability
that amino acid i mutates into amino acid j for all pairs of amino acids.
Such matrices are constructed by assembling a large and diverse sample of
verified pairwise alignments of amino acids. If the sample is large enough
to be statistically significant, the resulting matrices should reflect
the true probabilities of mutations occurring through a period of evolution.
(See also
A trademarked family of products that include databases, development tools, integration middleware, enterprise portals, and mobile and wireless servers.
On the same strand. The phrase “conserved synteny” refers to conserved gene order on chromosomes of different, related species.
BLAST Taxonomy Reports page. Tax BLAST groups BLAST hits by source organism,
according to information in
Taxonomy Identifier. The taxID is a stable unique identifier for each taxon
(for a species, a family, an order, or any other group in the taxonomy database).
The taxID is seen in the
See
One of three codons that do not specify any amino acid and hence causes translation of mRNA into protein to be terminated. These codons mark the end of a protein coding sequence.
An ordered list or map that defines a set of overlapping clones that covers a chromosome or other extended segment of DNA.
Third-Party Annotation
Tiling Path Format. A table format used to specify the set of clones
that will provide the best possible sequence coverage for a particular
chromosome, the order of the clones along the chromosome, and the location
of any gaps in the clone tiling path. Also used to refer to a file (Tiling
Path File) in which the
The position within an mRNA at which synthesis of a protein begins. The translation start site is usually an AUG codon, but occasionally, GUG or CUG codons are used to initiate protein synthesis.
Unique Identifier
See
UNIX is an operating system that was developed by Dennis Ritchie and
Kenneth Thompson at Bell Labs more than 30 years ago. It allows multitasking
and multiuser capabilities and offers portability with other operating systems.
It comes with hundreds of programs that are of two types: integral utilites, such
as the command line interpreter; and tools such as email, which are not necessary
for the operation of UNIX but provide additional capabilities to the user. It is
functionally organized at three levels: the kernel, which schedules tasks and
manages storage; the shell, which connects and interprets user's commands, calls
programs from memory, and executes them; and tools and applications, which offer
additional functionality to the operating system, such as word processing and
business applications. UNIX® was registered by
Uniform Resource Locator. The address of a resource on the Internet.
URL syntax is in the form of protocol://host/localinfo, where
“protocol” specifies the means of fetching the object
(such as HTTP, used by
UCS (Universal Character Set) Transformation Format. An AscII-preserving encoding method for Unicode (a standard to provide a unique number for every character irrespective of the platform, program, or language).
Untranslated Region. The 3′ UTR is that portion of an
An assignment of importance to a term in a search query. If a term in a search query is found to match a word in a document, that word is given a “weight”. The exact weight of the word will depend on the emphasis given to the word by the author or its position in the document. For example, a word that occurs in a chapter title will have a higher weight than the same word if it occurs in the body of the chapter. Similarly, words that occur in data collections are also assigned weights, depending on how frequently the terms occur in the collection.
Whole Genome Shotgun sequence. In this semi-automated sequencing technique, high-molecular-weight DNA is sheared into random fragments, size selected (usually 2, 10, 50, and 150 kb), and cloned into an appropriate vector. The clones are then sequenced from both ends. The two ends of the same clone are referred to as mate pairs. The distance between two mate pairs can be inferred if the library size is known and has a narrow window of deviation. The sequences are aligned using sequence assembly software. Proponents of this approach argue that it is possible to sequence the whole genome at once using large arrays of sequencers, which makes the whole process much more efficient than the traditional approaches.
World Wide Web. A
Extensible Markup Language. XML describes a class of data objects called XML documents and partially describes the behavior of computer programs that process them. XML is a subset of SGML, and XML documents are conforming SGML documents. XML documents are made up of storage units called entities, which contain either parsed or unparsed data. Parsed data is made up of characters (a unit of text), some of which form character data, and some of which form markup. Markup includes tags that provide information about the data, i.e., a description of the structure and content of the document. Character data comprises all the text that is not markup. XML provides a mechanism to impose constraints on the storage layout and logical structure.
Extensible Stylesheet Language. XSL is used for the transformation of
XML-based data into HTML or other presentation formats, for display in a
web browser. This is a two-part process. First, the structure of the input
XML tree must be transformed into a new tree (e.g., HTML), allowing
reordering of the elements, addition of text, and calculations—all
without modification to the source document. This process is described by
Extensible Stylesheet Language: Transformations. XSLT is a language
for transforming the structure of an XML document. XSLT is designed for
use as part of
Yeast Artificial Chromosome. Extremely large segments of DNA from another species spliced into the DNA of yeast. YACs are used to clone up to one million bases of foreign DNA into a host cell, where the DNA is propagated along with the other chromosomes of the yeast cell.
Zebrafish Information Network.