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Related Genomic Resources:
Literature Databases
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Nucleotide Databases
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Tools for 3D Structure Display and Similarity Searching
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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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