Hi everybody !
I'm working in order to create my own pairwise sequence alignment program in Python. I use the pairwise2.align command from Bipython. When I use it with small sequences it works. I put the code bellow (2 for a match, -2 for a mismatch, -3 for an open gap and -1 for an extend gap):
from Bio import pairwise2 target_seq = "ATGCNTGA" query_seq = "ATTGGCCATTN" alignments = pairwise2.align.globalms(target_seq, query_seq, 2, -2, -3, -1)
However when I used two huge sequence (HHV8 consensus sequence from an illumina sequencing), I got this error:
segmentation fault (core dumped)
I used the same code.
The size of sequences are:
cat ../Results/1G_S15/1G_S15.fasta | grep -v ">" | wc -c 140280 cat ../Results/8G_S12/1G_S12.fasta | grep -v ">" | wc -c 140272
Do you think that the huge sequence size can be the origin of this error ? If is the case, do you have a trick to avoid it ?