[Bioperl-l] [Gmod-schema] Circular genomes in Chado/BioPerl

Smithies, Russell Russell.Smithies at agresearch.co.nz
Tue Sep 9 16:46:26 EDT 2008


Excuse my ignorance (I'm not a biologist) but is it biologically possible/likely for a gene or feature to wrap more than once around a genome?
Anyone got an example?


Russell Smithies 

Bioinformatics Applications Developer 

Invermay  Research Centre 
Puddle Alley, 
Mosgiel, 
New Zealand 





> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-
> bio.org] On Behalf Of Lincoln Stein
> Sent: Wednesday, 10 September 2008 5:53 a.m.
> To: Aaron Mackey
> Cc: GMOD Schema List; Jim Hu; Roy Welch; bioperl-l at bioperl.org; Mike Gribskov
> Subject: Re: [Bioperl-l] [Gmod-schema] Circular genomes in Chado/BioPerl
> 
> It seems to me that the proposed modulus syntax handles multiple
> revolutions. Consider a 100 bp genome (to make it simple) and a feature that
> starts at 50, goes around twice, and ends at position 60:
> 
>   start = 50
>   end  = 260
> 
> length = end - start + 1
> revolutions = int (length/genome)
> stop position = length % genome + 1
> 
> Lincoln
> 
> On Mon, Sep 8, 2008 at 3:57 PM, Aaron Mackey <ajmackey at gmail.com> wrote:
> 
> > How can you handle features that may cross the origin more than once?
> > The modulus, though simple, seems to be only half the solution.  It
> > also makes it difficult to place features in the genome "by eye"
> > (having to do the modulus subtraction in my head), or in
> > sorting/filtering operations.
> >
> > I have an alternative that I wondered if you considered: allow the
> > start/end to have an additional "circular revolution" prefix:
> >
> > a typical range tuple like: 100 200 -
> > is thus shorthand for: 0:100 0:200 -
> > (i.e. both the 100 and 200 are in the same "revolution" around the genome)
> >
> > and is then distinguishable from an "around the genome + 100" feature of:
> > 1:100 0:200 -
> >
> > Just an alternative to consider (if you haven't already).  I'm not
> > wedded to the syntax, but I wouldn't want to see new columns in GFF
> > just for this.  Essentially, what you want is some form of compound
> > polar coordinates, it seems.
> >
> > -Aaron
> >
> > On Mon, Sep 8, 2008 at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
> > > In discussions with GMOD about Gbrowse, we've come up with a proposal for
> > > handling circular genomes and features that cross the origin in such
> > > genomes.  This applies to lots of prokaryotic and viral genomes, and
> > might
> > > be valuable for some ways of representing terminally redundant linear
> > > genomes.
> > > 1) Keep the requirement that start < end
> > > 2) allow end > parent feature length
> > > 3) parent feature gets an is_circular boolean
> > > 4) use modular arithmetic to calculate the real position of end on the
> > > parent feature.
> > > We'd like to do this in a way that will be consistent with Chado and
> > BioPerl
> > > representation of features as much as possible (realizing that there is
> > the
> > > usual interbase or not coordinate issue).  What do people think?  Lincoln
> > is
> > > on board for modifying the GFF3 spec.
> > > Thanks!
> > > Jim Hu
> > >
> > > =====================================
> > >
> > > Jim Hu
> > >
> > > Associate Professor
> > >
> > > Dept. of Biochemistry and Biophysics
> > >
> > > 2128 TAMU
> > >
> > > Texas A&M Univ.
> > >
> > > College Station, TX 77843-2128
> > >
> > > 979-862-4054
> > >
> > >
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> 
> 
> --
> Lincoln D. Stein
> 
> Ontario Institute for Cancer Research
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> 
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