[ensembl-dev] Using Ensemble to find TGFb1 and aligning sequence using ClustalW

[Giulietta]

Hi Paul,

The dev list is really for questions about the API, and local 
installations.  For questions along the lines of BLAST and how to decide 
which transcript to use, it may be better to email us at 
helpdesk at ensembl.org

The answer to your question depends on what you are trying to do. What 
is your hypothesis or the question you are trying to answer with your 
comparison?

Two out of the four splice variants are protein coding, as you can see 
in the Transcript Table at the top of Gene and Transcript views (like 
this one):

http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000105329;r=19:41807492-41859816;t=ENST00000221930

(TGFB1-001 and 004 are protein coding).

The first transcript (TGFB-001) is part of the CCDS set, meaning the 
coding sequence and protein sequence are agreed upon between several 
genomic projects.  In other words, TGFB-001 has a high quality (high 
confidence) coding sequence.

The second protein-coding transcript in the table (TGFB-004) is not in 
the CCDS.  If you look at the 'General identifiers' section of the 
Transcript Tab, you can find out what the transcript matches to (outside 
Ensembl)- in this case it's a TrEMBL cDNA:

http://www.ensembl.org/Homo_sapiens/Transcript/Similarity?db=core;g=ENSG00000105329;r=19:41807492-41859816;t=ENST00000598758

You can see the protein/cDNA sequence for each transcript in the cDNA 
link at the left of the Transcript Tab, which might allow you a more 
informed choice.

http://www.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?db=core;g=ENSG00000105329;r=19:41807492-41859816;t=ENST00000598758

Let us know (on helpdesk at ensembl.org) if you want to discuss this further.

Best wishes,
Giulietta (Ensembl Helpdesk)

On 20/04/2013 09:54, BASIL PAUL Ochieng wrote:
> Hi
> It my first time, exactly a week to use ensemble and do not have 
> bioinformatics skills.
> Could you please help me know which part of the sequence is to be 
> pasted and run for comparison.
> TGFB1 has 4 variants/transcripts,am i to paste and compare the 
> sequence of each variant on BLAST/ClustalW to compare with cDNA?
>
> Thanks
> Paul
> Immunogenetics course
> Manchester
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20130422/235cb731/attachment.html>