FASTA v36.3.5e (DNA and protein sequence alignment software)
The FASTA programs find regions of local or global (new) similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. Other programs provide information on the statistical significance of an alignment. Like BLAST, FASTA can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
FASTA includes the following binaries:
compares a protein sequence to another protein sequence or to a protein database, or a DNA sequence to another DNA sequence or a DNA library.
performs a rigorous Smith-Waterman alignment between a protein sequence and another protein sequence or a protein database.
compare a DNA sequence to a protein sequence database, translating the DNA sequence in three forward (or reverse) frames and allowing frameshifts.
evaluate the significance of pairwise similarity scores using a Monte Carlo analysis.