[Biojava-l] LocationTools + Decoratorated Locations = ?

[Schreiber, Mark]

Sorry to make it unclear,

It could be very useful but I can only think of that one example of where
you might want to do it. Essentially you are looking at renumbering the
coords of a larger plasmid which is the union of two smaller fragments. You
could then ask where do the two smaller fragments intersect the larger
fragment, all of which would be cool for plasmid mapping software (which I
guess is your interest)?

So I guess I have talked myself around to the idea that it would be useful,
but only in this instance. It could require some kind of Cloning API (which
would be useful) ie methods to join two circular sequences etc.
Alternatively you could linearize both sequences (remembering the point at
which they where linearized) then do the comparison.

Kudos if you can do it, circular coords give me a headache!


Mark Schreiber
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand

PH: +64 3 489 9175

 

> -----Original Message-----
> From: Cox, Greg [mailto:gcox@netgenics.com]
> Sent: Saturday, June 09, 2001 3:45 AM
> To: 'Schreiber, Mark'; 'biojava-l@biojava.org'
> Subject: RE: [Biojava-l] LocationTools + Decoratorated Locations = ?
> 
> 
> I'm not sure I understand what you're saying.  You question 
> why anyone would
> want to check overlaps of circular regions of different 
> length; and then you
> come up with the best use case I've seen for it.  
> 
> My reading is that you feel that's the only case, and it's 
> not strong enough
> to justify the headache of implementing this, is that accurate?
> 
> Greg
> 
> -----Original Message-----
> From: Schreiber, Mark [mailto:mark.schreiber@agresearch.co.nz]
> Sent: Thursday, June 07, 2001 7:47 PM
> To: 'Cox, Greg'; 'biojava-l@biojava.org'
> Subject: RE: [Biojava-l] LocationTools + Decoratorated Locations = ?
> 
> 
>  
> 
> > -----Original Message-----
> > From: Cox, Greg [mailto:gcox@netgenics.com]
> > Sent: Friday, June 08, 2001 9:15 AM
> > To: 'biojava-l@biojava.org'
> > Subject: [Biojava-l] LocationTools + Decoratorated Locations = ?
> > 
> > 
> > I'm feeling masochistic and ready to tackle the issue of how 
> > the location
> > semantics apply to decorated locations (currently circular 
> > and 'between'
> > locations).  
> > Circular Locations:
> > The problem:
> > 	Circular locations essentially redefine the coordinate 
> > system.  The
> > semantics are perfectly clear when dealing with locations 
> > that are circular
> > with the same circular length.  However, it's not clear what 
> > the result
> > should be when a location on a circular sequence of length 50 
> > is intersected
> > with a location on a circular sequence of length 40.  
> >
> 
> Excuse my ignorance but why on earth would you ever want to do this?
> 
> The physical aspects of circular sequences suggests that locations on
> sequences of differing lengths should not be allowed to intersect. One
> particular application might be where does location 700-900 
> lie on a new
> circular plasmid after  a 200 bp fragment has been inserted 
> at location
> 755-761. I think this is a little beyond the capabilities of the
> intersection/ union methods
>  
> Mark 
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