<div dir="ltr"><div><div><div><div><div><div>Thanks so much for your effort and response.<br></div><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></div>This makes it a challenge on what to report.<br>
</div>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></div>Thanks<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Apr 22, 2013 at 7:44 PM, Giulietta <span dir="ltr"><<a href="mailto:gspudich@ebi.ac.uk" target="_blank">gspudich@ebi.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<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 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 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 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 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 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)<div><div class="h5"><br>
<br>
On 20/04/2013 09:54, BASIL PAUL Ochieng wrote:<br>
</div></div></div>
<blockquote type="cite"><div><div class="h5">
<div dir="ltr">
<div>
<div>
<div>
<div>
<div>
<div>
<div>Hi<br>
</div>
It my first time, exactly a week to use ensemble and
do not have bioinformatics skills.<br>
</div>
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>
</div>
Thanks<br>
</div>
Paul<br>
</div>
Immunogenetics course<br>
</div>
Manchester<br>
</div>
<br>
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