Question: Genomic Change To Aa Change?
4
gravatar for Biomed
8.0 years ago by
Biomed4.5k
Bethesda, MD, USA
Biomed4.5k wrote:

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

sequence variant • 3.1k views
ADD COMMENTlink written 8.0 years ago by Biomed4.5k
5
gravatar for Sean Davis
8.0 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

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....

ADD COMMENTlink written 8.0 years ago by Sean Davis25k
1

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...

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by ostrokach280

+1 for annovar, great tool, easy to use

ADD REPLYlink written 8.0 years ago by Russh1.2k
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