NCBI常见术语(缩略词)详解

引用

NCBI

常见术语（缩略词）详解

3-D or 3D

Three- dimensional.

Accession number

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.

allele

One

of

the

variant

forms

of

a

gene

at

a

particular

locus

on

a

chromosome.

Different

alleles

produce variation in inherited characteristics such as hair color or blood type. In an

individual,

one

form

of

the

allele

(the

dominant

one)

may

be

expressed more

than

another

form (the

recessive

one).

When

―genes‖

are

considered simply

as segments

of

a nucleotide

sequence,

allele

refers to each of the possible alternative nucleotides at a specific position in

the

sequence.

For

example,

a

CT

polymorphism

such

as

CCT[C/T]CCAT

would

have

two

alleles

: C and T

.

API

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.

ASN.1

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.

BAC

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.

bit score

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:

a ―bit score‖ S′ is attained, which has a standard set

of units, and where K and

lambda

are

the statistical parameters of the scoring system. Because

bit scores

have been normalized with

respect to the scoring system, they can be used to compare alignment

scores from different

searches.

BLAST

Basic Local Alignment Search T

ool (

Altschul et al., J Mol Biol 215:403-410; 1990

). A sequence

comparison

algorithm

that is optimized for speed and used to search sequence databases for

optimal local alignments to a query. See the

BLAST

chapter (Chapter 15) or the

tutorial

or the

narrative

guide

to

BLAST

.

blastn

nucleotide

–

nucleotide

BLAST

.

blastn

takes

nucleotide

sequences

in

FASTA

format,

GenBankAccession numbers

, or

GI

numbers and compares them against the

NCBINucleotide

databases

.

blastp

protein

–

protein

BLAST

.

blastp

takes

protein

sequences in

FASTA

format,

GenBankAccession

numbers

, or

GI

numbers and compares them against the

NCBIProtein databases

.

BLAT

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.

BLA

T

on

proteins

finds sequences

of

80%

and

greater

similarity

of

length

20

amino acids or more.

BLA

T

is not

BLAST

. (See the

BLA

T web page

.)

BLOB

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.

build

A

run

of

the

genome

assembly

and

annotation

process

of

the

set

of

products

generated

by

that run.

CCAP

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

NCI

,

the

NCBI

,

and

numerous research labs.

CD

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.

CDART

Conserved

Domain

Architecture

Retrieval

T

ool.

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,

CDD

using

RPS- BLAST

.

CDD

Conserved

Domain

Database.

This

database

is

a

collection

of

sequence

alignments

and

profiles representing protein

domains

conserved during molecular evolution.

cDNA

complementary

DNA

.

A

DNA

sequence

obtained

by

reverse

transcription

of

a

messenger

RNA

(

mRNA

) sequence.

CDS

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.

CEPH

Centre d'Etude du Polymorphism Humain

CGAP

Cancer

Genome

Anatomy

Project.

CGAP

is

an

interdisciplinary

program

to

identify

the

human genes expressed in different cancerous states, based on

cDNA

< br>(

EST

) libraries, and to

determine the molecular profiles of normal, precancerous, and malignant cells. The

project

is a collaboration among the

NCI

, the

NCBI

, and numerous research labs.

CGH

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

in

situ

hybridization

(

FISH

).

DNA

extracted

from tumor cells is labeled in one color (e.g., green) and mixed in a 1:1 ratio with

DNA

from

normal cells, which is labeled in a different color (e.g., red). The mixture is then applied to

normal

metaphase

chromosomes.

Portions

of

the

genome

that

are

equally

represented

in

normal

and

tumor

cells

will

appear

orange,

regions

that

are

deleted

in

the

tumor sample

relative to the normal sample will appear red, and regions that are present in higher copy

number

in the

tumor

sample

(because

of

amplification)

will

appear

green.

Special

image

analysis tools are necessary to quantitate the ratio of green-to-red fluorescence to determine

whether a given region is more highly represented in the normal or in the tumor sample.

CGI

Common

Gateway

Interface.

A

mechanism

that

allows

a

W

eb

server

to

run

a

program

or

script on the server and send the output to a Web browser.

cluster

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

.

Cn3D

―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

structur e

–

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

Cn3D

homepage

provides

access

to

information

on

how

to

install the program, a tutorial to get started, and a comprehensive help document.

codon

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.

COGs

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

.

consensus sequence

The nucleotides or amino acids found most commonly at each position in the sequences of

homologousDNAs

,

RNAs

, or proteins.

contig

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.

Coriell

Coriell Institute of Aging Cell Repository

CPU

Central Processing Unit. The

CPU

is the computational and control unit of a computer

, the

device that interprets and executes instructions.

CSS

Cascading Style Sheets.

CSS

specify the formatting details that control the presentation and

layout of

HTML

and

XML

elements.

CSS

can be used for describing the formatting behavior

and text decoration of simply structured

XML

documents but cannot display structure that

varies from the structure of the source data.

Cubby

A tool of

Entrez

, the

Cubby

stores search strategies that may be updated at any time, stores

LinkOut

preferences to specify which

LinkOut

providers have to be displayed in

PubMed

, and

changes the default document delivery service.

DCMS

Data Creation and Maintenance System

DDBJ

DNA

Data Bank of Japan

definition line

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

example

);

also

DEFLINE,

as

in

a

flatfile.

DNA

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.

domain

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

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

BAC

clone (order and orientation of

the

fragments

are

unknown);

and

phase

2,

4

–

10×

coverage

of

a

BAC

clone

(order

and

orientation of the fragments are known). Phase 3 refers to the completely

finished sequence

.

DTD

Document T

ype 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.

DUST

A program for filtering low-complexity regions from nucleic acid sequences.

E-value

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

wit

h

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

tutorial

.

EC number

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

ENZYME

, the Enzyme nomenclature database, maintained at the

ExPASy

molecular

biology server.

EMBL

European Molecular Biology Laboratory

Entrez

Entrez

is

a

retrieval system

for

searching

several linked

databases. It

provides

access to

the

following

NCBI

databases:

PubMed

,

GenBank

,

Protein,

Structure,

Genome,

PopSet,

OMIM

,

T

axonomy, Books, ProbeSet, 3D

Domains

,

UniSTS

,

SNP

, and

CDD

. (See the

Entrez

chapter or

the

Entrez web page

.)

Entrez Gene

(formerly known

as

LocusLink).

Entrez

Gene

provides tracked,

unique

identifiers for

genes

(

GeneID

s)

and

reports

information

associated

with

those

identifiers

for unrestricted

public

use. See the

Entrez Genechapter

or

web page

.)

EST

Expressed

Sequence

T

ag.

ESTs

are

short

(usually

approximately

300

–

500

base

pairs),

single-pass sequence reads from

cDNA

. T

ypically, they are produced in large batches. They

represent the genes expressed in a given tissue and/or at a given developmental stage. They

are tags (some coding, others not) of expression for a given

cDNA

library. They are useful in

identifying full-length genes and in mapping.

e-PCR

Electronic

PCR

is used to compare a query sequence to mapped sequence-tagged sites (

STS

s)

to find a possible map location for the query sequence.

e-PCR

finds

STSs

in

DNA

sequences by

searching for subsequences that closely match the

PCR

primers present in mapped markers.

The

subsequences

must

have

the

correct

order,

orientation,

and

spacing

that

they

could

plausibly prime the amplification of a

PCR

product of the correct molecular

weight

.

epub citation

―Ahead

-of-

print‖

citation.

PubMed

now

accepts

citations

from

publishers

for

articles

that

have been published electronically ahead of the printed issue.

PubMed

displays the category

―[epub ahead

of print]‖ in the part of the citation where the volume and pagination would

ordinarily

display.

For

example:

Proc

Natl

Acad

Sci

U

S

A.

2000

May

2

[epub

ahead

of

print].

ExoFish

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

Tetraodon

nigroviridis

(similar

to

Fugu),

to

detect

conserved

sequences

with

a

very

low

background.

The

genome

of

T.

nigroviridis

is

eight

times

more

compact

than

the

human

genome

and

has

been used

in

the

comparative

identification

of

human

genes

from

the

rough

draft

of the

human

genome

(

Roest

Crollius

et

al.,

Nat

Genet

25:235-238; 2000

).

exon

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

intron

s or sometimes ―junk

DNA

‖) that often have no apparent

function but have been shown to encode small untranslated

RNAs

or regulatory information.

(See also

splice sites

.)

exon-trapped

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. T

otal

RNA

is isolated and reverse- transcribed. After

cDNA

synthesis and

PCR

amplification, the

exon

of interest is cloned.

ExPASy

Expert

Protein

Analysis

System

is

a

proteomics

server

of the

Swiss

Bioinformatics

Institute

(SIB).

FAST

A

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‖ (

Pearson and Lipman

). Also refers to a

format

for a nucleic acid or protein sequence.

fingerprint

The pattern of bands on a gel produced by a clone when restricted by a particular enzyme,

such as

Hin

dIII.

finished sequence

High-quality, low-error

DNA

sequence that is free of

gaps

. T

o qualify as a finished sequence,

only a single error out of every 10,000 bases (i.e., an accuracy of 99.999%) is allowed.

FISH

Fluorescence

in situ

hybridization. In this technique, fluorescent molecules are used to label a

DNA

probe, which can then hybridize to a specific

DNA

sequence in a chromosome spread so

that

the

site

becomes

visible

through

a

microscope.

FISH

has

been

used

to

highlight

the

locations of genes, subchromosome regions, entire chromosomes, or specific

DNA

sequences.

It

has

been

used

for

mapping

and

the

detection

of

genomic

rearrangements,

as

well

as

studies on

DNA

replication.

flatfile or flat file

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. T

o inte

rpret 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.

freeze

T

o 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.

FTP

File

T

ransfer

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.

gap

A

gap

is a space introduced into an alignment to compensate for insertions and deletions in

one

sequence

relative

to

another

.

T

o

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

figure

for more information.)

GB

gigabytes

GBFF

GenBank

Flat File. Refers to a format .gbff.

GenBank

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

EMBL

and

DDBJ

. [See the

GenBank

chapter (Chapter 1) or the

GenBank web page

.]

GeneID

GeneID

is a unique identifier that is assigned to a gene record in

Entrez Gene

. It is an integer

and

is

species

specific.

In

other

words,

the

integer

assigned

to

dystrophin

in

human

is

different

from

that

in

any

other

species.

For

genomes

that

had

been

represented

in

LocusLink, the

GeneID

is the same as the LocusID. The

GeneID

is reported in

RefSeq

records

as a 'db_xref' (e.g. /db_xref=

GeneID

:856646

GenBank

format).

genetic code

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

DNA

code; they stand for the chemicals adenine, thymine, guanine, and

cytosine, respectively, that make up the nucleotide bases of

DNA

. Each gene's code combines

the four chemicals in various ways to spell out three-

letter ―words‖ that specify which amino

acid is needed at every position for making a protein.

GenomeScan

A

gene

identification

algorithm

that

is

used

to

identify

exon

–

intron

structures

in

genomic

DNA

sequence.

genotype

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.

GEO

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

(

SAGE

)

data,

are

accepted,

accessioned,

and

archived

as

a

public

dataset.

[See

the

GEO

chapter

(Chpater 6) or the

GEO web page

.]

GI

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 n system of sequence identifiers (see the description

of

V

ersion

).

GSS

Genome Survey Sequences are analogous to

EST

s except that the sequences are genomic in

origin, rather than

cDNA

(

mRNA

). The

GSS

division of

GenBank

contains (but is not limited to)

the

following

types

of

data:

random

―single

-

pass

read‖

genome

survey

sequences,

cosmid/

BAC

/

Y