[Bioperl-l] problem with alignments and sequence locations

Steffen Heyne heyne at informatik.uni-freiburg.de
Tue Nov 10 07:55:06 EST 2009


I'm using Bioperl for my research and it is very useful! Thank you!

Currently I have a problem with locations tags of sequences. I read in 
seed alignments of Rfam (in stockholm format, but I think it is similar 
to other formats).

If the location is like:


the start/end values are changed to

$seq->start = 846
$seq->end = 908

and therefore the new location (e.g.$seq->get_nse) is:


The $seq->strand tag is correctly set to -1 in this case, but if the 
alignment is written out again (clustal, stockholm,...) this strand info 
is lost and the sequences have this "wrong" location. But this 
information is important in respect to the sequence accession number.

Is there a way to set the location back to the original one or is this 
behavior desired? Any manually setting with $seq->start($val) failed due 
to automatic checking.

I'm using bioperl 1.6.1



Steffen Heyne, Dipl.-Bioinf.
Lehrstuhl für Bioinformatik
Institut für Informatik
Albert-Ludwigs-Universität Freiburg
Georges-Köhler-Allee 106
79110 Freiburg, Germany

Tel: (+49) 761 203 8239
Fax: (+49) 761 203 7462
Mail: heyne at informatik.uni-freiburg.de

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