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<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>Where can I make Logo plot like follow?<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>Thanks.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'><img width=456 height=251 id="_x0000_i1025"
src="cid:image001.gif@01C59DF0.10D93770"></span><span lang=EN-US><o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>-----</span>邮件原件<span
lang=EN-US>-----<br>
</span>发件人<span lang=EN-US>:
bio_bulletin_board-bounces+ekeen=tongji.edu.cn@bioinformatics.org
[mailto:bio_bulletin_board-bounces+ekeen=tongji.edu.cn@bioinformatics.org] </span>代表
<span lang=EN-US>Iddo Friedberg<br>
</span>发送时间<span lang=EN-US>: <st1:chsdate
IsROCDate="False" IsLunarDate="False" Day="10" Month="8" Year="2005" w:st="on">2005<span
lang=EN-US><span lang=EN-US>年8</span></span><span lang=EN-US><span
lang=EN-US>月10</span></span><span lang=EN-US><span lang=EN-US>日</span></span></st1:chsdate>
6:12<br>
</span>收件人<span lang=EN-US>: The general forum at
Bioinformatics.Org<br>
</span>主题<span lang=EN-US>: Re: [BiO BB] Clustering small DNA
sequences into groups</span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>How about building a distance matrix of your own (based
on %ID between <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>fragments) and then use WEKA for the clustering?<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>./I<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>Samantha Fox wrote:<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>Thanks so much for your replies. However, it did
not work yet. cd-hit<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>gave this error, and blastclust is not usable for
such small sequences<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>!<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>Any suggestions ? <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>cat fasta<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>one<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>tagcgc<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>two<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>atcgtt<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>./cd-hit -i fasta -o www<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>total seq: 0<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>longest and shortest : 0 and 99999<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>Total letters: 0<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>terminate called after throwing an instance of
'std::bad_alloc'<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>> what(): St9bad_alloc<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>Abort (core dumped)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>./cd-hit -i fasta -o www -l 5<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>Fatal Error<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>Too short -l, redefine it<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>Program halted !!<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>On <st1:chsdate IsROCDate="False"
IsLunarDate="False" Day="5" Month="9" Year="2008" w:st="on">8/9/05</st1:chsdate>,
Martin Gollery <marty.gollery@gmail.com> wrote:<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>I believe those sequences are too short for
Blastclust. The default<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>word size is 32.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>Marty<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>On <st1:chsdate IsROCDate="False"
IsLunarDate="False" Day="5" Month="9" Year="2008" w:st="on">8/9/05</st1:chsdate>,
Marcos Oliveira de Carvalho <operon@cbiot.ufrgs.br> wrote:<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>>Hi Samantha,<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>>BLASTCLUST can group DNA sequences. Maybe
you will need to tweak the<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>>parameters (almost the same for BLAST). You
can get it at the NCBI ftp:<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>>ftp://ftp.ncbi.nih.gov/blast/<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>>cheers<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>>Marcos<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>>On Tue, 09 Aug 2005 14:24:41 -0300,
Samantha Fox <bioinfosm@gmail.com><o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>>wrote:<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>>>Hi,<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>>>I have a set of small DNA sequences
(about 40) 6-10 bp, and wish to<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>>>group them into clusters based on
sequence.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>>>Any suggestions for doing that ?<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>>>Thanks,<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>>>Samantha<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>>>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>_______________________________________________<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>Bioinformatics.Org general forum -
BiO_Bulletin_Board@bioinformatics.org<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>-- <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>Iddo Friedberg, Ph.D.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>The Burnham Institute<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=1 face=宋体><span lang=EN-US
style='font-size:9.0pt'>10901 N. Torrey <st1:Street w:st="on"><st1:address
w:st="on">Pines Rd.</st1:address></st1:Street><o:p></o:p></span></font></p>
<p class=MsoPlainText><st1:place w:st="on"><st1:City w:st="on"><st1:PersonName
ProductID="La Jolla" w:st="on"><font size=1 face=宋体><span
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