What's Your Problem? Open Thread
Welcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours.You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.
Hello,
I would like to know where can I find a tool that when I input SNP positions in some genes it will automatically output saying if it is a synonymous or non-synonymous mutation.
Best regards,
João Fadista
Hello João–
I’m going to start by recommending a couple of tools to try, but others may have more suggestions.
1. PolyPhen http://genetics.bwh.harvard.edu/pph/ which they describe as: “a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations” I can see their SNP2Prot link is broken today though, we will write to them today.
2. SIFT (Sorting Intolerant From Tolerant) http://blocks.fhcrc.org/sift/SIFT.html which they describe as: “SIFT predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations.”
You could do this in several other tools. The ones Mary suggested above tell you if they are predicted to have an affect on the structure and function of a protein (benign changes between amino acids or detrimental),
but if you just want to see if it’s synonymous vs. nonsynonymous, you could put in the rs number the snp into dbSNP, GVS (for Human) or UCSC Genome Browser and they’d all give you the position and detailed information about the SNP including whether it was synonymous or nonsynonmous.
But I assume you are looking for something more like deciding the possible effect? In that case Mary’s suggestions are good ones. There is also SNAP
FastSNP is another small but useful tool to find the function of SNPs in a gene or a single SNP ID and have them rated by “risk.”
Dear Mary and Trey,
Thanks a lot for the useful information. I will try the tools.
Best regards