Hi, I am just looking for some advice. I have to compare the ADN sequence of a gene extracted from 100 bacterial isolates. The bacterial isolates all belong to the same species, I just want to study if there is any differences in the sequence. I was thinking of align them. But maybe there is a less painful method within biopython or similar. I would like to use BLAST or any other website, I prefer to produce my own script. Can anyone give some advice here, please? Thanks,
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bio90029 •
The only problem I have is that I have about ~5000 genes, more or less the whole genome, to see.
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Sequence alignment for a single gene isn't 'painful'. It's really easy in such a simple case.
I wouldn't advise trying to actually do the alignment yourself (BioPython only has
Pairwise2baked in anyway AFAIK, and you need multiple sequence alignment.Just create a MSA using clustal (either via the GUI) or really easily via the commandline:
clustalo -i myseqs.fasta --outfmt phylip -o myresult.phy(or whatever alignment format you want to use).Thanks a lot. I will try both of the recommendations from you, and Sej Modha.
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