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As the number of DNA sequence data grows, it becomes harder for a single small site to make room for such databases. Fortunately, BLAST databases can be searched from a large number of websites around the world, running on servers dedicated to the purpose. A couple of good sites to look at for BLAST searches as well as other sequence tools are:

and last but not least,

The web-based approach avoids the problem of local databases becoming out-of-date, and links to remote databases becoming broken.

If you specifically need the alignment of two sequences at which the stand-alone version excelled, that too is covered by the NCBI under Blast 2 Sequences.

Local documentation for BLAST 2.0 is available on-line, but you should really use the online documentation from one of the websites.

An example of the FASTA format for sequences is here.

Note: If you publish results obtained from the use of BLAST please cite the following:

Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.

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Last Modified: Tuesday, 11-Mar-2003 13:56:02 EST by M. Strickler