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<DIV><FONT face=Arial size=2>I don't know of any conversion utilities but you
can certainly write a quick conversion in Perl. I'm not familiar with the
specific layouts but it sounds like you simply need to properly truncate each
row of data. There shouldn't be a problem if your field partition is white space
(or any other specific delimiter for that matter). </FONT></DIV>
<DIV><FONT face=Arial size=2>If you don't get a better offer, send me a small
data file of what you need converted, the field delimiter used, and an
example of what it needs converted into. I should be able to write you a Perl
routine and send it back to you. </FONT></DIV>
<DIV><FONT face=Arial size=2>Scott A. Halpine<BR>Ecologic Complex Systems,
LLC<BR>4640 Forbes Blvd, Suite 200<BR>Lanham, MD 20706-4885<BR>Phone:
301-918-3283<BR>Fax: 301-429-8762</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
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<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=A.Bossers@id.dlo.nl href="mailto:A.Bossers@id.dlo.nl">Bossers, A.</A>
</DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A
title=bio_bulletin_board@bioinformatics.org
href="mailto:bio_bulletin_board@bioinformatics.org">bio_bulletin_board@bioinformatics.org</A>
</DIV>
<DIV style="FONT: 10pt arial"><B>Cc:</B> <A
title=biodevelopers@bioinformatics.org
href="mailto:biodevelopers@bioinformatics.org">biodevelopers@bioinformatics.org</A>
</DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Tuesday, April 01, 2003 6:29
AM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> [BiO BB] Clustering EST
sequences</DIV>
<DIV><BR></DIV>
<P><FONT face="News Gothic" size=2>Dear All,</FONT> </P>
<P><FONT face="News Gothic" size=2>I have a very basic problem of which I
wonder how others have solved this.</FONT> </P>
<P><FONT face="News Gothic" size=2>I want to make a unigene collection of a
large EST database. We have chromat files in ABI format and I use Linux on the
intel platform.</FONT></P>
<P><FONT face="News Gothic" size=2>I have phred and phrap running but since
phrap was originally designed for genomic sequences we get lots of
misaasemblies on poly-A or poly-T stretches.</FONT></P>
<P><FONT face="News Gothic" size=2>Therefore I installed the TIGR tigcl
package which is designed for EST databases and also runs very well on multi
node machines.</FONT></P>
<P><FONT face="News Gothic" size=2>However, it uses multi fasta files (and
corresponding (optional) quality files) as input.</FONT> <BR><FONT
face="News Gothic" size=2>I wanted to use the phred package to generate the
required fasta and qual files. This runs fine but the fasta file has in the
>name line additional info separated with spaces. These files are not
accepted by TGICL.</FONT></P>
<P><FONT face="News Gothic" size=2>Is there an easy unix (linux) utility to
convert these multi fasta files and quality fasta files in simpel >name
{CRT} seq files so they kan be used as input for tgicl? Or is a conversion
utility available to convert/extract phreds phd files into fasta-seq and
fasta-qual?</FONT></P>
<P><FONT face="News Gothic" size=2>Any help would be appreciated,</FONT> </P>
<P> <FONT face="News Gothic"
size=2>Alex</FONT> </P><BR></BLOCKQUOTE></BODY></HTML>