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How can I search a batch of sequences with ...

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How can I search a batch of sequences with BLAST?

There are three options for "Batch" BLAST searches:

1) Web MegaBLAST EST analysis tool: This program is optimized for aligning nucleotide sequences that differ slightly as a result of sequencing or other similar "errors". MegaBLAST is good for scanning a large number of EST type sequences (about 500 kb in length) against large database in search of the closest matches. You can import a file EST sequences in FASTA format or as a list of GenBank accessions or/GIs and have them compared to the BLAST databases. The default is an easily reviewable Hit Table format, although you can download and save the results in Standard pairwise HTML or any of the other result output options. MegaBLAST is available from the BLAST web page, the standalone BLAST executables, or via the network BLAST client (see below).

2) Standalone BLAST executables:The Standalone BLAST executables are command line programs which run BLAST searches against local downloaded copies of the NCBI BLAST databases. The programs will handle either a single large file with multiple FASTA query sequences, or you can create a script to send multiple files one at a time. The executables are available for a wide variety of platforms, including many "flavors" of UNIX (LINUS, Solaris, etc.) Windows PC and even Mac OSX.

The Standalone executables are available at the anonymous FTP location: There is information on the Standalone BLAST executables available in the README file at which is also bundled with the downloaded binaries.

3) BLAST Network Client 'blastcl3':The BLAST 2.0 Network client will allow you to submit a single file of FASTA sequences over an internet connection to the NCBI BLAST databases. You submit searches through the client to the NCBI servers and do not need to download the database locally. The BLAST Network client executables are located at: There are blastcl3 executables for various UNIX platforms, PC Windows and Macintosh.

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