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In the ever changing world of bioinformatics, the two most popular programs for sequence similarity searching, Basic Local Alignment Search Tool (BLAST) and FASTA, have both recently been improved. BLAST Version 2.0 is now available at the National Center for Biotechnology Information (NCBI) Web site, and FASTA 3.0 is available both as free software for most computer systems and on several Web servers. Iterative Neighborhood Cluster Analysis (INCA) is a Java applet that runs a series of BLAST searches to collect all sequences that are similar to a query sequence.

Advanced Similarity Searches on the Web: Gapped BLAST, PSI-BLAST, FASTA 3.0 and INCA