[Bioperl-l] Getting clustalw alignments in a form codeml can use

Jason Stajich jason at cgt.duhs.duke.edu
Wed Jun 23 09:14:30 EDT 2004

Build a simple align - that is what AlignIO gives you back.  You need to
build one from the data you got back from the database.

my $simplealn = Bio::SimpleAlign->new();

my $i=0;
for my $seq ( @seqstringfromdatabase ) {
 my $lseq = Bio::LocatableSeq->new(-seq => $seq,
			           -display_id => $yourids[$i++]);

pass the $simplealn to PAML.


On Tue, 22 Jun 2004, Julian M Catchen wrote:

> Hello,
> Can someone help me with the following problem? I am aligning sequences using
> clustalw and then storing the text strings from the alignment individually in
> a database. I want to then pull these sequences from the database and feed
> them to PAML::codeml, but I can't figure out what object to load them into
> that codeml will understand. I can see how to add them to Bio::Seq objects,
> but what do I do with them after that? It appears to me that codeml requires
> a Bio::AlignI object in order to execute.
> I have previously written the clustal alignments out to a file and then used
> an Bio::AlignIO object to read them in and give me my Bio::AlignI object for
> codeml, but I would like to do this entirely within the database and I would
> prefer not dumping a verbatim clustal file into the database. Anyone have any
> ideas?
> Thanks in advance for any help,
> julian

Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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