PC/GENE: Database Searches

Generally, when a new sequence is found, it is important to know if all or parts of it are similar to other known sequences. This can be done by using the new sequence to search for similarity to sequences in a database. The PC/GENE package contains two programs, FSTNSCAN and FSTPSCAN, for searching nucleic acid and protein databases, respectively. Both programs are based on the search algorithms of Lipman and Pearson (1 ). These programs determine a numerical score for sequence similarity and can impose gaps in the sequences to optimize alignments.