how to assign snp to gene and gene to pathway using KEGG database ? any software available?

Question

[reneesummer]

Hi,

Any one had experience of extracting membership of snps to genes and genes to pathway using KEGG data base? If we have the location of snps, how can we know what gene it belongs to and also what is its corresponding pathway that this particular gene belongs to?

Since genetic data is huge and it's not possible for me to do one by one. Can any one offer me some guidance? Thanks so much!

Answer 1

[kautilya]

I would recommend using the SeattleSeq Annotation server. It accepts input in a variety of formats including a custom one which you can specify yourself. It will add Gene and KEGG pathway annnotations for your submitted snps along with a lot of additional annotations if required.

[reneesummer]

thanks so much! this look awesome. studying it now.