Thanks Jennifer That future snp->protein change tool sounds great to me.
I'll also look at Galaxy. -Archie On Mon, Feb 1, 2010 at 11:44 AM, Jennifer Jackson <[email protected]> wrote: > 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> > <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
