Genomic Change To Aa Change?

Question

[Biomed]

I have a set of genomic coordinates and genomic sequence changes (i.e g.Agenomicposition_C ). I need to find in which transcripts and what corresponding amino acid changes will occur as a result of this genomic sequence variation from the reference. Can you please direct me to the right resource. I would generally like to use UCSC tables, pythoin/biopython for this and it should be a standalone solution as opposed to going to a web site/service etc.
A link to a protocol, tutorial or even a chapter from a bioinformatics book that covers this subject for future reference would also be very much appreciated. Sorry for the basic question but I don't have any other bioinformaticians around me so you guys are my first step.

Thanks

Answer 1

[Sean Davis]

Here are a few standalone tools:

• http://snpeff.sourceforge.net/
• http://www.openbioinformatics.org/annovar/
• ftp://ftp.ensembl.org/pub/misc-scripts/Variant_effect_predictor_1.0/
• http://sift.jcvi.org/

The list could probably go on....

[ostrokach]

Annovar requires a license from Biobase for commercial use and is written in perl. SNPeff is open source, licensed under LGPLv3, is written in Java, and integrates with GATK and Galaxy...

[Russh]

+1 for annovar, great tool, easy to use