<span style="font-family: arial,sans-serif; color: rgb(255, 0, 0);">Hi Alex,</span><br style="font-family: arial,sans-serif; color: rgb(255, 0, 0);"><br style="font-family: arial,sans-serif; color: rgb(255, 0, 0);"><span style="font-family: arial,sans-serif; color: rgb(255, 0, 0);">
Thank you so much for your reply.</span><br style="font-family: arial,sans-serif; color: rgb(255, 0, 0);"><br style="font-family: arial,sans-serif; color: rgb(255, 0, 0);"><span style="font-family: arial,sans-serif; color: rgb(255, 0, 0);">
How do you generate the unigene list after assembling the ESTs?</span><br style="font-family: arial,sans-serif; color: rgb(255, 0, 0);"><br style="font-family: arial,sans-serif; color: rgb(255, 0, 0);"><span style="font-family: arial,sans-serif; color: rgb(255, 0, 0);">
Thanks again!</span><br style="font-family: arial,sans-serif; color: rgb(255, 0, 0);"><br style="font-family: arial,sans-serif; color: rgb(255, 0, 0);"><span style="font-family: arial,sans-serif; color: rgb(255, 0, 0);">Ahmed
</span><br style="font-family: arial,sans-serif; color: rgb(255, 0, 0);"><br><div><span class="gmail_quote">On 8/11/06, <b class="gmail_sendername">Bossers, Alex</b> <<a href="mailto:Alex.Bossers@wur.nl">Alex.Bossers@wur.nl
</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>









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<p><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;">Ahmed,</span></font></p>

<p><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>

<p><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB">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></p>

<p><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB"><a href="http://www.tigr.org/tdb/tgi/software/" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
http://www.tigr.org/tdb/tgi/software/</a></span></font></p>

<p><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB">For basecalling I used a
windows platform based caller since PHRED at that time did not support our used
dyes for sequencing.. :(</span></font></p>

<p><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB">Thereafter the TGICL basically
uses megablast to cluster all sequences into groups and than assembles it using
the cap3 assembler.</span></font></p>

<p><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB"> </span></font></p>

<p><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB">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></p>

<p><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB"> </span></font></p>

<p><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB">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" onclick="return top.js.OpenExtLink(window,event,this)">http://www.tigr.org/tdb/tgi/index.shtml</a></span></font>
</p>

<p><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB"> </span></font></p>

<p><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB"> </span></font></p>

<p><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB">Now the next steps.</span></font></p>

<p><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB"> </span></font></p>

<p><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;" lang="EN-GB">Alex</span></font></p></div></div></div></blockquote></div>