[Open-bio-l] Best practice for modelling data in GFF

[Chris Fields]

All,

Appears that link isn't up to date.  Current GFF3 spec (v. 1.16, updated May 25) here:

http://www.sequenceontology.org/gff3.shtml

chris

On May 28, 2010, at 12:06 PM, Jason Stajich wrote:

> It's covered in the GFF3 spec as match_part if that helps.
> http://song.sourceforge.net/gff3.shtml
> 
> Dan Bolser wrote, On 5/28/10 9:29 AM:
>> Hi guys,
>> 
>> Not sure if this is the right forum, but I just thought I'd ask...
>> 
>> Where can I find information on 'best practices' for modelling
>> biological data in GFF?
>> 
>> For example, I'd like to model paired-end sequence alignments in GFF.
>> One suggestion was to use match/match_part to link each end into a
>> pair. Another option is to use 'read_pair' with 'contig' for the
>> parent feature...
>> 
>> Should I just be using SAM/BAM?
>> 
>> Seems a shame not to have a standard way to do this in GFF...
>> 
>> 
>> Cheers,
>> Dan.
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>> Open-Bio-l at lists.open-bio.org
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>>   
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