Hi Archie, A tool is under development to do a stand-alone analysis, but it is not ready to share yet. Likely, it will operate on SNPs and UCSC Genes (at least, possibly other genePred tracks) and provide information about how the change impacts the transcript/translated protein (syn/non-syn, impacts splicing, etc.). Whether the SNPs must come from dbSNP or can be user defined (in a custom track) is not decided yet.
Meanwhile, you could try some of the tools at Galaxy. Here is some input from them: "Mutate Codons with SNPs" tool under "Evolution" section on Galaxy should help to answer this question. The output of the tool will consist of codons in the input mutated with the respective SNPs. To check if the changes are synonymous or not, the user can join this output with a tabular file containing the genetic code using "Join two queries" tool under "Join, subtract and group" section. Guru, Galaxy team. Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Archie Russell" <[email protected]> wrote: > From: "Archie Russell" <[email protected]> > To: "Jennifer Jackson" <[email protected]> > Cc: [email protected] > Sent: Friday, January 29, 2010 11:39:58 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] snp->protein change > > Thanks -- the function is definitely useful for known SNPs, but what > if I'm > starting with a novel SNP in genomic coordinates? > > > On Fri, Jan 29, 2010 at 11:34 AM, Jennifer Jackson <[email protected]> > wrote: > > > Hello again, > > > > We have another table/file to suggest: > > > > snp130CodingDbSnp -- it has more detailed functional annotations > provided > > by dbSNP > > > > Thanks, > > Jennifer > > > > > > ------------------------------------------------ > > Jennifer Jackson > > UCSC Genome Bioinformatics Group > > > > ----- "Jennifer Jackson" <[email protected]> wrote: > > > > > From: "Jennifer Jackson" <[email protected]> > > > To: "Archie Russell" <[email protected]> > > > Cc: [email protected] > > > Sent: Friday, January 29, 2010 11:05:33 AM GMT -08:00 US/Canada > Pacific > > > Subject: Re: [Genome] snp->protein change > > > > > > Hello, > > > > > > Using the dbSNP track controls or the primary table itself, > > > Coding - Synonymous and Coding - Non-Synonymous > > > is an annotated for some of the data in this location: > > > > > > snp130.func > > > > > > http://genome.ucsc.edu/FAQ/FAQdownloads#download1 > > > http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html > > > > > > You can also take any transcript (full or coding only), > > > swap in the variation, and use this tool to do a translation: > > > http://genome.ucsc.edu/ -> Utilities (left blue navigation bar) -> > DNA > > > Duster > > > > http://users.soe.ucsc.edu/~kent/dnaDust/dnadust.html<http://users.soe.ucsc.edu/%7Ekent/dnaDust/dnadust.html> > > > > > > Jennifer > > > > > > ------------------------------------------------ > > > Jennifer Jackson > > > UCSC Genome Bioinformatics Group > > > > > > ----- "Archie Russell" <[email protected]> wrote: > > > > > > > From: "Archie Russell" <[email protected]> > > > > To: [email protected] > > > > Sent: Friday, January 29, 2010 10:50:06 AM GMT -08:00 US/Canada > > > Pacific > > > > Subject: [Genome] snp->protein change > > > > > > > > Hi guys > > > > > > > > If I zoom in close enough using the browser I see there are > amino > > > > acid > > > > residues for each gene, is there a tool or suggested method to > > > > determine > > > > how a particular SNP effects these residues? > > > > > > > > Thanks > > > > Archie > > > > _______________________________________________ > > > > Genome maillist - [email protected] > > > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
