[EMBOSS] (no subject)
uludag at ebi.ac.uk
Wed Nov 12 17:22:28 UTC 2008
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
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
> 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.
> 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
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