Hi Brooke Thanks for a quick revert. It is good to know that someone previously had asked about this problem. Sorry if my initial mail was not clear, I meant our own SNP predictions from Next Generation Sequencing Data.
So as an input we have hg18/NCBI36.2 bp location of SNP. We then want to know whether a predicted SNP is syn/non-syn. Ideall we want to implement this as an automated service. Indeed the thread explain the biology quite nicely how this could be done. It is not very clear from the second part of the explanation which talks about how this could be done in an automated fashion. I have couple of questions about the basic workflow and how the UCSC genome browser data could be used. So when Jennifer talks about downloading the (mRNA and protein )sequence and substituting the SNP base(s). The downstream analysis is more oriented towards manual inspection of the results. 1. Any specific method which could on the fly classify a particular SNP position to be syn/non-syn. 2. Also how to substitute the SNP bp position in a mRNA transcript. I belv the coordinates will differ due to introns/intergenic regions. Thanks for your patient reading. Your pointers in this direction shall help us a great deal. Cheers! -Abhi -----Original Message----- From: Brooke Rhead [mailto:[email protected]] Sent: Tuesday, July 07, 2009 9:31 PM To: Pratap, Abhishek Cc: [email protected] Subject: Re: [Genome] About SNP classification Hello Abhishek, Thank you for searching the mailing list archives! Are you referring to your own SNP predictions, or the SNPs in the SNP track on the Genome Browser (from dbSNP)? If you are referring to the SNP track, you can find information on a SNP's predicted functional role in the 'func' field of the SNP table (such as the snp129 table for the hg18 assembly). Note that non-synonymous changes are denoted by words other than "non-synonymous". A full description of the possible classifications for the 'func' field is on the SNP track details page (http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=snp129). Here is an excerpt: # Coding - Synonymous - no change in peptide for allele with respect to reference assembly (coding-synon) # Coding - Non-Synonymous - change in peptide for allele with respect to reference assembly (nonsense, missense, frameshift) These annotations are done by dbSnp, based on RefSeq Genes. Indel information is in the 'class' field of the SNP table. Again, more details are available on the SNP track details page. The locations of SNPs in genomic coordinates are available in the chrom, chromStart and chromEnd fields. We do not have information on the position of SNPs within genes; however, there are other annotations in the 'func' field that describe a SNP's position in a gene, such as locus region, intron, untranslated, splice site, etc. If you are instead referring to your own SNP predictions, perhaps this previous mailing list response is what you are looking for: https://lists.soe.ucsc.edu/pipermail/genome/2009-May/018897.html I hope this is helpful. If you have further questions, please feel free to email us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 07/07/09 08:45, Pratap, Abhishek wrote: > Hi All > > > > This might seem to be an old track question. However I was not able to > find a good answer in the mailing list archives. > > > > For all our SNP predictions we would like to know whether they are > synonymous / non-synonymous. If Non-synonymous/Exonic then find the > position on the gene where amino acid is getting changed and to what > ...Also info about indels will help. > > > > It will be great if you could give me some pointers. > > > > > > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences <http://www.igs.umaryland.edu/> > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > > Chair > RSG-Worldwide <http://iscbsc.org/rsg> > ISCB-Student Council <http://iscbsc.org/> > > > > > > > > > > > > Thanks, > > -Abhi > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
