Being A Beginner A Simple Question To All Of You....I

Question

[jha.deepraj]

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????

[Sean Davis]

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

[Neilfws]

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

Answer 1

[Sean Davis]

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.