The program performs pairwise sequence alignment of two protein sequences or two DNA sequences depending on the user's configuration of parameters. It can also perform global sequence alignment, semi-global sequence alignment, and local sequence alignment depending on the user's configuration. The program chooses the corresponding scoring matrix - dnaMatrix or BLOSUM45 - file depending on if it is a protein sequence alignment or DNA sequence alignment.
Parameters for the program:
-i First sequence [File In and should be FASTA format]
-j Second sequence [File In and should be FASTA format]
-p Align protein sequences or DNA sequences [T/F]
-atype global, or semi-global [G/S]
-o alignment output file [File Out]
Possible ways of running the program - align.py.
• $python3 align.py -i seq1.txt -j seq2.txt -o out.txt -p F -atype G
Perform global pairwise sequence alignment of two DNA sequences in seq1.txt and
seq2.txt. The output will be in out.txt.
• $python3 align.py -i seq1.txt -j seq2.txt -o out.txt -p T -atype S
Perform semi-global pairwise sequence alignment of two protein sequences in seq1.txt and
seq2.txt. The output will be in out.txt.
The order of the parameters does not matter. For example:
$python3 align.py -i seq1.txt -j seq2.txt -o out.txt -p F -atype G
&
$python3 align.py -i seq1.txt -j seq2.txt -p F -atype G -o out.txt