[Bioperl-l] Problems with circular genomes
jimhu at TAMU.EDU
Wed Sep 14 21:31:49 EDT 2005
Most bacterial and many viral genomes are circular. Some, like T4 are
physically linear but circularly permuted, giving a circular genetic
is_circular is a flag that is settable and gettable (I think) in
BioPerlBio::PrimarySeqI. Although Lincoln emailed me that he thinks
there is a workaround for this for GBrowse, I haven't been able to
figure out how to be able to scroll the viewer around the circle.
Worse, I have no clue about how to handle features that cross the
circle junction. It's not clear to me how it can be done within the
current GFF3 format.
It's not enough to be able to specify a circular genome, one has to
be able to specify which way a feature goes around the circle. Note
that one can NOT assume that features will always go the short way
around... the late mRNAs for many viruses are very, very long, and a
transposon inserted in a small plasmid can be bigger than the parent
plasmid. It seems to me that either an additional column should be
used for direction (right or left relative to start), or the
constraints on start and end should be relaxed so that if start>end
and is_circular is true the feature goes around the circle across the
This is also a problem in the lightweight annotation file format for
external uploads, where there are only three required columns and the
start..end relationship is used to specify strand, not direction.
I suspect that this has been addressed before, but I wasn't able to
figure it out from the archives or the docs...but then I'm not a
programming wizard by a long shot. I did find this message on Bio-SQL
archive (via Google) from Hilmar Lapp:
But I didn't see a resolution.
Associate Professor and Associate Head for Graduate Programs
Dept. of Biochemistry and Biophysics
Texas A&M Univ.
College Station, TX 77843-2128
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