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<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Ahmed,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>In our case the
unigenelist is the list we ended-up with after assembling (so basically the
singletons and contigs). To make it more complete into a unigenelist we did a
second round of clustering assembling after we added the entries with which we
had a BLAST hit at nr/nt database (excluding the BAC clones etc). Hereby we
also grouped contigs/singletons that where not overlapping in our dataset yet.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Alex<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
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<p class=MsoNormal><b><font size=2 face=Tahoma><span lang=EN-GB
style='font-size:10.0pt;font-family:Tahoma;font-weight:bold'>Van:</span></font></b><font
size=2 face=Tahoma><span lang=EN-GB style='font-size:10.0pt;font-family:Tahoma'>
bio_bulletin_</span></font><font size=2 face=Tahoma><span style='font-size:
10.0pt;font-family:Tahoma'>board-bounces+alex.bossers=wur.nl@bioinformatics.org
[mailto:bio_bulletin_board-bounces+alex.bossers=wur.nl@bioinformatics.org] <b><span
style='font-weight:bold'>Namens </span></b>Ahmed Moustafa<br>
<b><span style='font-weight:bold'>Verzonden:</span></b> vrijdag 11 augustus
2006 23:00<br>
<b><span style='font-weight:bold'>Aan:</span></b> <st1:PersonName w:st="on">Bossers,
Alex</st1:PersonName><br>
<b><span style='font-weight:bold'>CC:</span></b> bio_bulletin_board@bioinformatics.org<br>
<b><span style='font-weight:bold'>Onderwerp:</span></b> Re: [BiO BB] Starting
point EST annotation/grouping</span></font><o:p></o:p></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3 color=red
face=Arial><span style='font-size:12.0pt;font-family:Arial;color:red'>Hi Alex,<br>
<br>
Thank you so much for your reply.<br>
<br>
How do you generate the unigene list after assembling the ESTs?<br>
<br>
Thanks again!<br>
<br>
Ahmed </span></font><o:p></o:p></p>
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<p class=MsoNormal><span class=gmailquote><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>On 8/11/06, <st1:PersonName w:st="on"><b><span
style='font-weight:bold'>Bossers, Alex</span></b></st1:PersonName> <<a
href="mailto:Alex.Bossers@wur.nl">Alex.Bossers@wur.nl </a>> wrote:</span></font></span><o:p></o:p></p>
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<p><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'>Ahmed,</span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'> </span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'>No I did not use the PHRED/PHRAP/CONSED package
for this (I did try it but found the TGICL suite more appropriate for ESTs).</span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'><a href="http://www.tigr.org/tdb/tgi/software/"
target="_blank">http://www.tigr.org/tdb/tgi/software/</a></span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'>For basecalling I used a windows platform based
caller since PHRED at that time did not support our used dyes for sequencing..
:(</span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'>Thereafter the TGICL basically uses megablast to
cluster all sequences into groups and than assembles it using the cap3
assembler.</span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'> </span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'>Clustering and assembling is always difficult to
explain. As far as I understand the clustering of large groups of sequences
speeds up the second step; assembling. Basically you end up with contigs
(having more than one sequence) or singletons.</span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'> </span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'>With unigene list I mean a list of all different
genes present in my sample of 13k. Like the Gene indices lists of species
present at TIGR. <a href="http://www.tigr.org/tdb/tgi/index.shtml"
target="_blank">http://www.tigr.org/tdb/tgi/index.shtml</a></span></font><span
lang=EN-GB> </span><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'> </span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'> </span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'>Now the next steps.</span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'> </span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'>Alex</span></font><o:p></o:p></p>
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