Dear Mahmut,
The Eponine regions would be TSS predicted by the Eponine program. This
is different from the Ensembl Perl API approach Harpreet mentioned (e.g.
use the API to get each Ensembl mRNA and see if its predicted start
codon is at the beginning or not). It's fair to say both approaches will
get you predictions, but different ones, due to different methodology
used to generate the predictions.
Best wishes,
Daniel.
Mahmut Uludag wrote:
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
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