NCBI数据库与工具

文献类:

PubMed :Biomedical literature citations and abstracts生物医学文献引文和摘要

PubMed Central :Free, full text life sciences articles完整的文献

OMIM :Online Mendelian Inheritance in Man articles on human genes and phenotypes人类孟德尔遗传

Books: Online biomedical texts在线书籍

Organism:

Taxonomy :Organisms represented in the NCBI sequence databases

Sequence

Nucleotide GenBank, EMBL, DDBJ, PDB, RefSeq, TPA, and patented nucleotide sequences

Protein Translations of GenBank, EMBL, and DDBJ records, as well as PDB, PIR, PRF, SWISSPROT

and patented protein sequences

PopSet Sets of sequences from population, phylogenetic and mutation studies

Trace Archives Raw sequence traces generated by large sequencing projects

Genome

Genome Complete Genome records integrated with sequence, genetic and physical maps

dbSNP Single nucleotide polymorphism as well as insertion, deletion and microsatellite

information

UniSTS Sequence Tagged Site marker and mapping data

Gene Summary pages of Gene-centered information

HomoloGene Computationally-determined homologs among eukaryotic organisms with complete

genomes

Expression

GEO Gene Expression Omnibus, a repository for gene expression and hybridization array data

UniGene Gene-based clusters of EST and mRNA sequences

Structure

CDD Conserved Domain Database for identified protein domains

CDART Modular domain architecture of proteins

MMDB/Structure Experimental 3D structure data from PDB

PubChem Information on small molecule chemical compounds and substances assayed for

biological activity

SEARCH METHODS

ENTREZ

The Entrez database structure and search protocol integrates the scientific literature, taxonomy,

sequence, genome, expression and structure data into a tightly interlinked system.

(www.ncbi.nlm.nih.gov/Entrez/)

BLAST

Basic Local Alignment Search Tool (BLAST) is a sequence similarity search program that can be used via

a web interface or as a stand-alone tool. BLAST compares combinations of nucleotide or protein queries

to sequences in nucleotide or protein databases and provides statistical information to help decipher the

biological significance of the alignment. (www.ncbi.nlm.nih.gov/BLAST/)

VAST

Vector Alignment Search Tool (VAST) is a structure similarity search service. VAST compares the 3D

organization of secondary structures of protein structures to those in the MMDB/Structure database and

allows for viewing superpositions and alignments using Cn3D.

(www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html)

SELECTED TOOLS

Sequin A stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank,

EMBL, or DDBJ sequence databases (www.ncbi.nlm.nih.gov/Sequin/)

VecScreen Quick identification of nucleic acid sequence that may be due to vector contamination

(www.ncbi.nlm.nih.gov/VecScreen/)

MapViewer Integrated views of sequence, genetic and physical chromosome maps for eukaryotic organisms

(www.ncbi.nlm.nih.gov/mapview/)

ePCR Scanning of DNA sequence for sequence tagged sites in our UniSTS database

(www.ncbi.nlm.nih.gov/sutils/e-pcr/)

Model Maker View evidence for gene annotations on assembled genomic sequence, and create your own model

transcripts (www.ncbi.nlm.nih.gov/mapview/static/ModelMakerHelp.html)

Spidey Alignments of one or more mRNA sequences to a single genomic sequence (www.ncbi.nlm.nih.gov/spidey)

ORFinder Predictions of all possible ORFs in an RNA sequence (www.ncbi.nlm.nih.gov/gorf/)

Digital Differential

Display

Comparisons of mRNA levels in different cell-lines, tissues and organs

(www.ncbi.nlm.nih.gov/UniGene/info_ddd.html)

SAGEmap Gene expression results from SAGE tags mapped to mRNA sequences in GenBank

(www.ncbi.nlm.nih.gov/projects/SAGE/)

Cn3D

A helper application for web browsers that allow for simultaneous viewing of 3D structures with sequence

alignments. Also has powerful annotation and alignment editing features.

(www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml)

The BLAST Suite

A sequence similarity search program that compares nucleotide or protein queries to sequences in

nucleotide or protein databases and provides statistical information to help decipher the biological

significance of the alignment. It can be used via a web interface or as a stand-alone tool.

(www.ncbi.nlm.nih.gov/BLAST/)

The NCBI BLAST ftp site provides standalone blast, client server blast, and wwwblast packages for

different platforms. It also provides commonly used blast databases in preformatted as well as FASTA

format. (ftp://ftp.ncbi.nih.gov/blast/)

Programming Tools & Information

Batch Entrez Upload a file of UIDs or accession numbers to retrieve records

(www.ncbi.nlm.nih.gov/entrez/batchentrez.cgi?)

E-Utilities Guidelines for Entrez “URL calls” used to access data at NCBI by scripts

(eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html)

NCBI Toolkit

The NCBI Software Development Toolkit was developed for the production and distribution of GenBank,

Entrez, BLAST, and related services by NCBI. Source code is provided as well as information on NCBI’s

data model, data encoding and programming libraries. (www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit)

Creating Weblinks

General Entrez Links www.ncbi.nlm.nih.gov/entrez/query/static/linking.html

OMIM page Links www.ncbi.nlm.nih.gov/Omim/omimhelp.html#HowToLink

UniGene page Links www.ncbi.nlm.nih.gov/UniGene/FAQ.html

Structure page Links www.ncbi.nlm.nih.gov/Structure/MISC/linking.html#mmdbsrv

Taxonomy page Links www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=howlink

NCBI Handbook

Individual chapters describing databases, major search algorithms and data processing

pipelines; each describes the database design or how the resource works and how the

different databases and resources relate to each other, along with a brief overview on

using the resource. (www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=handbook)

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