[DAS] Locations between bases

[Ed Griffiths]

Hi Thomas,

A while ago I spent some time trying to persuade the GFF version 3 people not to 
use base positions to code this difference as it leads to ambiguity. I failed 
but I would urge you not to use positions to do it but instead have some other 
data that indicates that what you want is the position between two bases.

Ed


On Mon, 7 Mar 2011, Thomas Down wrote:

> The day has come when I find I need to be able to distinguish between a
> feature which actually *covers* one or a small number of bases (e.g. a SNP)
> and a feature which refers to a point between two bases (e.g. an
> insertion).  Have any other DAS folk dealt with this before, and if so how?
> One possible approach would be something like:
>
>         <START>30000000</START>
>         <STOP>29999999</STOP>
>
> ...as a way to reference the position between the 29999999th and 30000000th
> bases in a sequence... but is this going to break lots of existing client
> code?
>
> (I also rather dislike it because there's currently sanity-checking code in
> Dazzle to stop you doing stuff like this...)
>
> Any better ideas?
>
>            Thomas.
>
> PS. Yes, I'm aware this is a solved problem in DAS/2.  Afraid I need a DAS/1
> solution, though.
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das
>

-- 
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| Ed Griffiths, Acedb/ZMap development, Informatics Group,               |
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| email: edgrif at sanger.ac.uk  Tel: +44-1223-496844  Fax: +44-1223-494919 |
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