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<div class="moz-cite-prefix">On 22/04/2013 19:11, BASIL PAUL Ochieng
wrote:<br>
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<div>Thanks so much for your effort and response.<br>
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<div>I got a way of saving the sequence as FAST on a
notepad/ and running the BLAST for nucleotide
sequence, cDNA etc<br>
</div>
The task had no specific scope.It was just to look for
as much information as we could on TGFb1.<br>
</div>
I wish i had the restriction of the search to give to
you.<br>
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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).<br>
<br>
That's as much as I can help you with in regards to this problem.<br>
<br>
Please email <a class="moz-txt-link-abbreviated" href="mailto:helpdesk@ensembl.org">helpdesk@ensembl.org</a> with this type of question in the
future (not <a class="moz-txt-link-abbreviated" href="mailto:dev@ensembl.org">dev@ensembl.org</a>).<br>
<br>
Good luck with your report!<br>
<br>
Cheers,<br>
Giulietta<br>
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<div>This makes it a challenge on what to report.<br>
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Could you please help me with the information on how to
report (lab report) the Ensembl search and result!<br>
</div>
This seems weird but is my first time to learn on my own and
use bioinformatics for the distance program am taking.<br>
<br>
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Thanks<br>
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<div class="gmail_extra"><br>
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<div class="gmail_quote">On Mon, Apr 22, 2013 at 7:44 PM,
Giulietta <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:gspudich@ebi.ac.uk" target="_blank">gspudich@ebi.ac.uk</a>></span>
wrote:<br>
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<div>Hi Paul,<br>
<br>
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 <a moz-do-not-send="true"
href="mailto:helpdesk@ensembl.org" target="_blank">helpdesk@ensembl.org</a><br>
<br>
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?<br>
<br>
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):<br>
<br>
<a moz-do-not-send="true"
href="http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000105329;r=19:41807492-41859816;t=ENST00000221930"
target="_blank">http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000105329;r=19:41807492-41859816;t=ENST00000221930</a><br>
<br>
(TGFB1-001 and 004 are protein coding).<br>
<br>
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.<br>
<br>
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: <br>
<br>
<a moz-do-not-send="true"
href="http://www.ensembl.org/Homo_sapiens/Transcript/Similarity?db=core;g=ENSG00000105329;r=19:41807492-41859816;t=ENST00000598758"
target="_blank">http://www.ensembl.org/Homo_sapiens/Transcript/Similarity?db=core;g=ENSG00000105329;r=19:41807492-41859816;t=ENST00000598758</a><br>
<br>
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.<br>
<br>
<a moz-do-not-send="true"
href="http://www.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?db=core;g=ENSG00000105329;r=19:41807492-41859816;t=ENST00000598758"
target="_blank">http://www.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?db=core;g=ENSG00000105329;r=19:41807492-41859816;t=ENST00000598758</a><br>
<br>
Let us know (on <a moz-do-not-send="true"
href="mailto:helpdesk@ensembl.org" target="_blank">helpdesk@ensembl.org</a>)
if you want to discuss this further.<br>
<br>
Best wishes,<br>
Giulietta (Ensembl Helpdesk)
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<div class="h5"><br>
<br>
On 20/04/2013 09:54, BASIL PAUL Ochieng wrote:<br>
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<div>Hi<br>
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It my first time, exactly a week to
use ensemble and do not have
bioinformatics skills.<br>
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Could you please help me know which part
of the sequence is to be pasted and run
for comparison.<br>
</div>
TGFB1 has 4 variants/transcripts,am i to
paste and compare the sequence of each
variant on BLAST/ClustalW to compare with
cDNA?<br>
<br>
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Thanks<br>
</div>
Paul<br>
</div>
Immunogenetics course<br>
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Manchester<br>
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