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.

My NCBI

My NCBI saves searches and results and features an option to automatically update and e-mail search results from your saved searches.

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.

Stand-alone BLAST

Download BLAST executables for local use. For more information on how BLAST works, its output, and how both the output and program itself can be further manipulated or customized, see the BLAST section of the NCBI Handbook.

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.

TaxPlot

Provides a three-way comparisons of genomes on the basis of the protein sequences they encode.

Sequence Submission

Sequin

A data submission tool that includes ORF Finder, an alignment viewer/editor, and a link to PowerBLAST. See the GenBank Submission Page for general submission information.

BankIt

WWW submission tool for one or simple sequence submissions.