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<P><FONT SIZE=2 FACE="News Gothic">Dear All,</FONT>
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<P><FONT SIZE=2 FACE="News Gothic">I have a very basic problem of which I wonder how others have solved this.</FONT>
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<P><FONT SIZE=2 FACE="News Gothic">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 SIZE=2 FACE="News Gothic">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 SIZE=2 FACE="News Gothic">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 SIZE=2 FACE="News Gothic">However, it uses multi fasta files (and corresponding (optional) quality files) as input.</FONT>
<BR><FONT SIZE=2 FACE="News Gothic">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 SIZE=2 FACE="News Gothic">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 SIZE=2 FACE="News Gothic">Any help would be appreciated,</FONT>
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<P> <FONT SIZE=2 FACE="News Gothic">Alex</FONT>
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