[DAS] Locations between bases

[Lincoln Stein]

Hi All,

The GFF3 convention is to make start==end and to have the flagged insertion
occur to the right of the designated base.

The elegant way to do this is to use Jim Kent's convention of half-open
spans, in which case the coordinates apply to the position BETWEEN bases,
but this causes too much confusion to satisfy a relatively rare requirement.

Lincoln

On Mon, Mar 7, 2011 at 8:02 AM, Ed Griffiths <edgrif at sanger.ac.uk> wrote:

> 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
>>
>>
> --
>  ------------------------------------------------------------------------
> | Ed Griffiths, Acedb/ZMap development, Informatics Group,               |
> |  The Morgan Building, Sanger Institute, Wellcome Trust Genome Campus   |
> |  Hinxton, Cambridge CB10 1HH                                           |
> |                                                                        |
> | email: edgrif at sanger.ac.uk  Tel: +44-1223-496844  Fax: +44-1223-494919 |
>  ------------------------------------------------------------------------
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research Limited,
> a charity registered in England with number 1021457 and a company registered
> in England with number 2742969, whose registered office is 215 Euston Road,
> London, NW1 2BE. _______________________________________________
>
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das
>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>