If anyone else on the list is also interested to know how to get TSS information using Ensembl I forward Harpreet's message below. Harpreet told me "Eponine regions" feature should be used to get TSS information for Humans.
Regards, Mahmut On Wed, 2008-11-12 at 16:46 +0000, Harpreet Saini wrote: > Hi Mahvash, > > I have used Ensembl web site many times to get the information about > the transcription start sites (TSS). You can get the TSS from the > features link in the Ensembl genome browser for your organism of > interest. > The other thing is that you can also easily obtain the start/end of > mRNA and coding regions from the Ensembl database using the Perl API. > If you have not used Ensembl or perl API before, then the ensembl web > site have very nice tutorials for beginners. > > Hope this will help you. > > Regards > Harpreet > > On 12 Nov 2008, at 16:38, Mahmut Uludag wrote: > > > Hi Mahvash, > > > >> iam a bioinformatics student and workin in linux .. my project is on > >> coxepression of genes in humans ... but i dont know much abt java.. > >> as java > >> is the language which linux supports and not csharp.. > >> i wanted to compare the start of mrna and coding regions to check the > >> presence or absence of TSS ... > > > > I talked to a colleague from the EBI RNA genomics group about your > > question. Harpreet told me you can do these comparisons using the > > Ensembl web site. I now forward your message to Harpreet. (If she > > can't > > post her answer to the emboss list, as she is not a member on the > > list, > > I will try posting on her behalf) > > > > Regards, > > Mahmut > > > >> if anyone can help i will be really grateful.. > >> thanks > >> mahvash > > > > Harpreet Kaur Saini > Enright Group > EMBL-European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > Tel: +44-(0) 1223-492676 > > > > _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
