This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Determine The Position Of A Snp In A Multiple Sequence Alignment

Hi BioStars
I have a bunch of pairwise sequence alignments (simple clustal alignments).
One of the sequences is the reference sequence. I would like to extract the position of the SNPs.
I wrote some code in python, allowing me to extract the position of the SNP in the alignment. Given that position I extracted the 10nt upstream of the SNP and used those 10nt to search the reference sequence. Doing that I was able to get the position of the SNP in the reference. This approach seemed to work well, however I was wondering whether anyone had a solution that would be more elegant?
I would be happy to share my code if people are interested

python snp
• 4,216 views • link
written by Whetting Whetting

1 answer

I wrote a couple of python scripts that do the job. They are not annotated (which is why I am not sharing them) but if you are interested in these files, just let me know!!

• 0 views • link
written by Whetting Whetting

Can you send me the python scripts that you mentioned in your post? I am doing the job that you described in your post.

• 0 views • link
written by health • health

Log in to answer this question.

More posts like this