On Fri, Feb 10, 2012 at 9:14 PM, Abhishek Pratap <apratap at="" lbl.gov=""> wrote: > Hi Sean > > I see. I was wondering if I can scan my sequences against InterPro > (EBI) and get the GO information from there. Any package in > bioconductor or may be I need to use their API. I don't think Bioc has that, but I'd love to hear otherwise. You can certainly try Interpro, but in your situation, I'd be working toward mapping your sequences to a rich data source like Entrez Gene or Ensembl. There are a number of routes to that goal, but all of them start with some sequence similarity searching. Sean > On Fri, Feb 10, 2012 at 6:10 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >> On Fri, Feb 10, 2012 at 7:48 PM, Abhishek Pratap <apratap at="" lbl.gov=""> wrote: >>> Unfortunately the gene id's are local to us. ?So there will be no >>> mapping between them to RefSeq, Entrez etc. >> >> Assuming that you mean that you do not have GenBank or any other >> public ID, I see no option for you except to start BLASTing to get >> some useful ID. >> >> Sean >> >> >>> On Fri, Feb 10, 2012 at 4:45 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >>>> On Fri, Feb 10, 2012 at 3:50 PM, Abhishek Pratap <apratap at="" lbl.gov=""> wrote: >>>>> Chlamydomonas. ?I was reading a bit more about this ..so I guess what I >>>>> might need to do is associate GO ID for each gene in my set and the may be >>>>> use GOSeq like packages but I am not sure how should I go about associating >>>>> GO ID's to genes. >>>> >>>> And what, exactly, are your gene ids? ?Are they Entrez Gene IDs, >>>> RefSeq, Genbank, or something else? >>>> >>>>> On Fri, Feb 10, 2012 at 12:46 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >>>>> >>>>>> What organism? >>>>>> >>>>>> On Fri, Feb 10, 2012 at 2:48 PM, Abhishek Pratap <apratap at="" lbl.gov=""> wrote: >>>>>> > We have identified a set of genes to be differentially expressed between >>>>>> > treatment and control. ?The current gene annotation doesnt have >>>>>> functional >>>>>> > information about the gene. >>>>>> > >>>>>> > What we would like to do is asses the biological functions of these >>>>>> genes( >>>>>> > may be based on GO and then cluster them). I was wondering if there is >>>>>> > something already out there to do so in semi automated way. >>>>>> > >>>>>> > I am thinking of blasting them against pfam ?or be myhits dbase but >>>>>> wanted >>>>>> > to take your opinion. >>>>>> > >>>>>> > PS ?: cross posted on biostar mailing list : >>>>>> > >>>>>> http://biostar.stackexchange.com/questions/17332/functional- assessment-of-genes >>>>>> > >>>>>> > Thanks! >>>>>> > -Abhi >>>>>> > >>>>>> > ? ? ? ?[[alternative HTML version deleted]] >>>>>> > >>>>>> > _______________________________________________ >>>>>> > Bioconductor mailing list >>>>>> > Bioconductor at r-project.org >>>>>> > https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> > Search the archives: >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>> >>>>> >>>>> ? ? ? ?[[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor