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<p class=MsoNormal>Sheldon McKay,<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>My name is Jonathan Shao and I believe I met you at PAG. I
saw your demo and I am trying to implement the gbrowse_syn program.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>How do I generate meaningful clustal alignments?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>case 1: have contigs and want to align them to a completed
genome<o:p></o:p></p>
<p class=MsoNormal>Do you blast the contigs against the completed genome and then
use clustalw on that isolated region?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>case2: align 2 completed genomes<o:p></o:p></p>
<p class=MsoNormal>Do you slice/cut up one of the completed genomes into
defined sequence lengths and blast each sequence against a completed genome?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Is blast the method of choice or are that other programs
that would be better for aiding in creating the alignments for clustalW?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>##############################################################################<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Do you have sample data with corresponding contig files that
I can work with? I did see the wormbase gbrowse_syn, but I am not sure how you
generated the alignments. Also, I did not see a sample config file for gbrowse_syn.
<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Any advice you can give me would be appreciated. <o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Thanks in advance,<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Sincerely,<o:p></o:p></p>
<p class=MsoNormal>Jonathan Shao <o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
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