FASTY
FastY does a Pearson/Lipman search for similarity between a nucleotide query sequence and a group of protein sequences, taking frameshifts into account. It is designed to answer the question, "What protein sequences encoded by my nucleic acid sequence are homologous to sequences in a specified protein database(s) ?" FASTX and FASTY are similar programs. FASTX uses a simpler, faster algorithm for alignments that allows frameshifts only between codons. FASTY is slower but produces better alignments with poor quality sequences because frameshifts are allowed within codons. Part of the FastA family.
For more about fastx, fasty, tfastx, tfasty, see: Pearson WR, Wood T, Zhang Z, Miller W. (1997) "Comparison of DNA sequences with protein sequences." Genomics. Nov 15;46(1):24-36.
Manual: http://www.med.nyu.edu/rcr/rcr/fastaman.html
INPUT = Nucleic Acid sequence files in fasta format. The search set is either a single protein sequence or multiple protein sequences. You can specify multiple sequences.
TEST INPUT FILES
Input file: fasty_in.txt
TEST OUTPUT FILES
Output file: fasty_out.txt