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<DIV dir=ltr align=left><FONT face=Arial color=#0000ff size=2><SPAN
class=244352216-31052006>If you happen to have perl and bioperl installed, you
can convert myfile.pfam to myfile.pfam.fa with the following unix
one-liner:</SPAN></FONT></DIV>
<DIV dir=ltr align=left><FONT face=Arial color=#0000ff size=2><SPAN
class=244352216-31052006></SPAN></FONT> </DIV>
<DIV dir=ltr align=left><FONT face=Arial color=#0000ff size=2>cat myfile.pfam |
perl -MBio::AlignIO -e 'select Bio::AlignIO->newFh(-format => "fasta");
$in = Bio::AlignIO->newFh(-format => "pfam", -fh => \*STDIN); print
while <$in>' > myfile.pfam.fa</FONT></DIV>
<DIV dir=ltr align=left><FONT face=Arial color=#0000ff
size=2></FONT> </DIV>
<DIV dir=ltr align=left><FONT face=Arial color=#0000ff
size=2></FONT> </DIV><BR>
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<FONT face=Tahoma size=2><B>From:</B>
bio_bulletin_board-bounces+mec=stowers-institute.org@bioinformatics.org
[mailto:bio_bulletin_board-bounces+mec=stowers-institute.org@bioinformatics.org]
<B>On Behalf Of </B>Iain Wallace<BR><B>Sent:</B> Wednesday, May 31, 2006 5:34
AM<BR><B>To:</B> bio_bulletin_board@bioinformatics.org<BR><B>Subject:</B> [Bio
BB] Convert PFAM to FASTA<BR></FONT><BR></DIV>
<DIV></DIV>Hi all,<BR><BR>Does anyone know of a programme that can take a pfam
alignment and convert it into fasta?<BR><BR>Thanks <BR><BR>Iain
<BR><BR></BLOCKQUOTE></BODY></HTML>