Question: python tools for aligning and translating subsequences containing SNPs
gravatar for vdjonsson
2.9 years ago by
vdjonsson0 wrote:

I am trying to develop a pipeline that will align a large number of subsequences of a certain length surrounding SNPs to the human genome, and then translate those subsequences to amino acid representations. I figure this should be straightforward using biopython and/or standard tools. However, I am not sure what the best way to do this is, and was wondering if I could get some insight into some of people's favorite tools.

sequencing snp python • 683 views
ADD COMMENTlink modified 2.9 years ago by WouterDeCoster40k • written 2.9 years ago by vdjonsson0
gravatar for WouterDeCoster
2.9 years ago by
WouterDeCoster40k wrote:

I'm not sure why you would like to do this in python. You probably need an aligner, a variant caller, and a tool like VEP or SnpEff to annotate these variants.

ADD COMMENTlink written 2.9 years ago by WouterDeCoster40k

Thanks for your comment, I'm just really looking for the best tools. I already have the location of the SNP, I just need to extract a surrounding subsequence, align it and translate it. I will look into the tools you mention, thanks!

ADD REPLYlink written 2.9 years ago by vdjonsson0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 849 users visited in the last hour