This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Being A Beginner A Simple Question To All Of You....I

i am confused with a lot of softwares and different formats into action....can anyone suggest me the method to detect snp's and effected protein functionalities in lung cancer (lung squamous carcinoma cell)..the data is available fron TCGA in xml format....a solution in python language and how biopython community helps us in achieving the same????

snps cancer biopython python
• 1,918 views • link
updated by Biostar Biostar • written by jha.deepraj • jha.deepraj

Which software generated the output? Blast?

• 0 views • link
written by Phil S. Phil S.

It would be great if you could provide a URL or a set of steps that you used to get your data.

• 0 views • link
written by Sean Davis Sean Davis

This is not really a simple question. And I hope that "a solution in python language" != "write my code for me".

• 0 views • link
written by Neilfws Neilfws

1 answer

Assuming that you have variants in VCF format (a common format for describing variants in the genome), you can use one of several softwares for determining the effect on protein. Commonly-used packages include snpEff, Ensembl Variant Effect Predictor (VEP), and Annovar; there are many others.

• 0 views • link
written by Sean Davis Sean Davis

Log in to answer this question.

More posts like this