[EMBOSS] (no subject)

Daniel Barker db60 at st-andrews.ac.uk
Wed Nov 12 17:55:45 UTC 2008

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,


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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Daniel Barker
The University of St Andrews is a charity registered in Scotland :
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