[Bioperl-l] problem with alignments and sequence locations
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
79110 Freiburg, Germany
Tel: (+49) 761 203 8239
Fax: (+49) 761 203 7462
Mail: heyne at informatik.uni-freiburg.de
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