SeqAlign

Advanced Algorithmics project It is a command line tool for global and local pairwise and multiple sequence alignment.For global alignment we implemented Needleman-Wunsch algorithm and for local Smith-Waterman algorithm. Then we extended those algorithms to work with >2 sequences by the usage of heuristic algorithm named progressive alignment. Additionally, we added several additional features for tuning (25 different substitution matrices, adjustable gap penalty) and exploration (sub-region extraction, antibody framework extraction and DNA-protein-DNA conversion). See –help to see all the parameters. In order to use –extract_fw ANARCI tool needs to be installed from http://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/ANARCI.php