[Bioperl-l] Location mapping question

Cook, Malcolm MEC at stowers-institute.org
Wed Nov 9 16:50:56 EST 2005

Hows this strategy:

assuming the 'maf' alignments produced by blat (gfClient) are legible to
Bio::AlignIO (are they?)

and you get your $mRNA2genome and $oligo2mRNA alignments in this 'maf'
format (can you?)

you can then read them into memory with Bio::AlignIO (which purports to
read 'maf' format)

and then step over the Bio::LocatableSequence $oligo_sequence in the
oligo2mRNA alignment(s)

using bioperl's $oligo_sequence ->column_from_residue_number to get each
oligos start and end positions in the mRNA alignment

and $oligo2mRNA->location_from_column to translate the start and end
position into a coordiante on the mRNA

then use the same technique to map these positions through the
mRNA2genome alignment into genomic coordinates

Shouldn't be too hard.  I've done something like it to map insertion
mutations to reference sequences (though not depending on 'maf' format
as interlingua).


Malcolm Cook - mec at stowers-institute.org - 816-926-4449
Database Applications Manager - Bioinformatics
Stowers Institute for Medical Research - Kansas City, MO  USA 

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Sean Davis
Sent: Wednesday, November 09, 2005 12:18 PM
To: Bioperl
Subject: [Bioperl-l] Location mapping question

I think I have seen code to do this kind of thing--hence this email--but
may be mistaken.  I have oligo sequences mapped to mRNAs by blat and
blat alignments to the genome.  Is there a way to quickly align the
to the genome given this information using a bioperl module.  (Like I
I just can't seem to find it).


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