Question: Determine The Position Of A Snp In A Multiple Sequence Alignment
2
gravatar for Whetting
5.7 years ago by
Whetting1.5k
Bethesda, MD
Whetting1.5k wrote:

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 • 2.2k views
ADD COMMENTlink written 5.7 years ago by Whetting1.5k
1
gravatar for Whetting
5.7 years ago by
Whetting1.5k
Bethesda, MD
Whetting1.5k wrote:

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!!

ADD COMMENTlink written 5.7 years ago by Whetting1.5k

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

ADD REPLYlink written 4.6 years ago by health0
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