Another option is the SNP consequence tool in Ensembl. On an Ensembl Location page:
http://www.ensembl.org/Homo_sapiens/Location/View?r=6:133017695-133161157 click on "Manage your data" and select the SNP Effect predictor. This unsurprisingly works off Ensembl Genes. The functionality is also available in the Ensembl API On 1 Feb 2010, at 20:02, Archie Russell wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
