BLAST

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:

• NCBI at the NIH.
• ExPASy at the Swiss Institute of Bioinformatics.

and last but not least,

• a local collection of many nifty genomics tools, courtesy of the Gerstein laboratory.

The web-based approach avoids the problem of local databases becoming out-of-date, and links to remote databases becoming broken.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

An example of the FASTA format for sequences is here.

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.