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

BASIL PAUL Ochieng talk2pbasil at gmail.com
Mon Apr 22 19:11:44 BST 2013


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.
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> 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
>
> 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/
>
>
>
> _______________________________________________
> 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/fcc53ac5/attachment.html>


More information about the Dev mailing list