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TOOLS FOR DATA MINING

Various data retrieval and submission tools may be found on the NCBI Web site, including:

Text Term Searching

 

Entrez:

Provides integrated access to nucleotide and protein sequence data from over 100,000 organisms, along with three-dimensional protein structures, genomic mapping information, and PubMed MEDLINE.

 

LinkOut:

A registry service to create links from specific articles, journals, or biological data in Entrez to resources on external Web sites.

 

Cubby:

Allows Entrez users to store and update searches and to customize their LinkOut display to include or exclude links to providers.

 

Citation Matcher:

Allows you to find the PubMed ID or the MEDLINE UID of any article in the PubMed database, given its bibliographic information.

 

Sequence Similarity Searching

 

BLAST Homepage:

Access to BLAST (Basic Local Alignment Search Tool) programs, overview, help documentation, and FAQs.

 

BLink:

Displays the results of BLAST searches that have been done for every protein sequence in the Entrez Protein database.

 

BLAST E-mail server:

The BLAST e-mail server was discontinued on June 17, 2002. Click here for further information.

 

Network-Client BLAST:

A BLAST client (blastcl3) that accesses the NCBI BLAST search engine. Blastcl3 can search all the sequences in a FASTA file and produce one-to-many alignments in text or HTML format. It can also perform searches against multiple databases.

 

Stand-alone BLAST:

Download BLAST executables for local use.

 

Taxonomy

 

Taxonomy Browser:

A tool for searching NCBI's taxonomy database.

 

Taxonomy BLAST:

Groups BLAST hits by source organism according to their classification in NCBI's Taxonomy database.

 

TaxTable:

Summarizes BLAST taxonomy data and displays the relationship of the organism to others through a color-coded graph.

 

ProtTable:

Provides a summary of protein coding regions in a genome.

 

TaxPlot:

Provides a three-way view of genome similarities.

 

Sequence Submission

 

Sequin:

A data submission tool that includes ORF Finder, an alignment viewer/editor, and a link to PowerBLAST.

 

BankIt:

WWW submission tool for one or simple sequence submissions.

 
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