FASTA

FASTA is a software tool designed to search protein sequences efficiently and selectively in large libraries. It achieves high speed by initially focusing on amino acid identities, allowing it to search the NBRF protein sequence library in under 20 minutes on an IBM-PC microcomputer. The program's sensitivity is enhanced by using the PAM250 matrix and a joining step to calculate the initial score, aiding in detecting proteins with a common ancestor billions of years ago. Compared to NWS-based programs, FASTA is considerably faster, slightly less sensitive, and more selective.

FASTA proves helpful in identifying protein sequences descended from a common ancestor, particularly in cases where the search results yield a list of homologous sequences or sequences with similarity scores indistinguishable from the library's bulk. However, the tool may not always provide clear-cut results, necessitating careful analysis of similarity scores, statistical significance, aligned residues, and biological context.