Needleman Wunsch Sequence alignment

Implementation of Needleman-Wunsch sequence alignment algorithm

Running from terminal

Without matched regions

python3 needleman_wunsch.py -q query_sequence_file -r reference_sequence_file

The query sequence is human protein sequence, and the reference sequence is the fly protein sequence. Thus, for alignment of HOX protein the following command should be given:

python3 needleman_wunsch.py -q Human_HOX.fa -r Fly_HOX.fa

Alignment of PAX protein sequence in human and fruit fly

Anchored version

Anchored alignment of protein sequences in human and fruit fly can be run by adding a file specifying matched regions at the end.

python3 needleman_wunsch.py -q query_sequence_file -r reference_sequence_file -m matched_regions