To align protein sequences, smart ways of comparing have to be developed. This program implements a sequence alignment algorithm, as well as mutlithreading. It was written by Sacha Verheeke, Cécile Castiaux and Hassan Nehme.

Sources:

[1] M S Farrar - NCBI BLAST Database Format (2010).pdf [2] T Rognes - Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation.pdf [3] O Gotoh - An improved algorithm for matching biological subsequences.pdf [4] T Smith and M Waterman - Identification of common molecular subsequences.pdf

How to start the program?

1)Compilation: make 2)Execution: ./gotoh Database* Query_Sequence BLOSUM_Matrix gap_open_penalty gap_extend_penalty

For example: $./gotoh uniprot_sprot.fasta P00533.fasta BLOSUM62.txt 11 1

PS: make sure that the following files are in the directory where the program is beeing executed!

1 query sequence file. 2 The database files: pin, psq and phr. 3 BLOSUM matrix file.