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 <[email protected]> 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 >> [email protected] >> 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: [email protected] 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 > [email protected] > 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 <[email protected]> _______________________________________________ DAS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/das
