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

[Giulietta]

On 22/04/2013 19:11, BASIL PAUL Ochieng wrote:
> Thanks so much for your effort and response.
> I got a way of saving the sequence as FAST on a notepad/ and running 
> the BLAST for nucleotide sequence, cDNA etc
> The task had no specific scope.It was just to look for as much 
> information as we could on TGFb1.
> I wish i had the restriction of the search to give to you.
If I were you, I would BLAST each cDNA separately.  Then report on the 
top hits for each cDNA, and mention which ones are protein coding and 
which ones are not (As in my previous message).

That's as much as I can help you with in regards to this problem.

Please email helpdesk at ensembl.org with this type of question in the 
future (not dev at ensembl.org).

Good luck with your report!

Cheers,
Giulietta
> This makes it a challenge on what to report.
> Could you please help me with the information on how to report (lab 
> report) the Ensembl search and result!
> This seems weird but is my first time to learn on my own and use 
> bioinformatics for the distance program am taking.
>
> Thanks
>
>
> On Mon, Apr 22, 2013 at 7:44 PM, Giulietta <gspudich at ebi.ac.uk 
> <mailto:gspudich at ebi.ac.uk>> wrote:
>
>     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 <mailto: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
>     <mailto: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 listDev at ensembl.org  <mailto:Dev at ensembl.org>
>>     Posting guidelines and subscribe/unsubscribe info:http://lists.ensembl.org/mailman/listinfo/dev
>>     Ensembl Blog:http://www.ensembl.info/
>
>
>     _______________________________________________
>     Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>     Posting guidelines and subscribe/unsubscribe info:
>     http://lists.ensembl.org/mailman/listinfo/dev
>     Ensembl Blog: http://www.ensembl.info/
>
>
>
>
> _______________________________________________
> 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/20130423/f2322c1b/attachment.html>