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

[Leighton Pritchard]

Hi Dan,

On 28/05/2010 Friday, May 28, 17:29, "Dan Bolser" <dan.bolser at gmail.com>
wrote:

> 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?

The specification is a good place to start:

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

> 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...

I'm not sure it's an issue with GFF as much as it is just working out where
your data fits in the Sequence Ontology model.

If your read pairs have been used to assemble the larger contig sequence
that you're modelling them as part_of, then read_pair would seem to be
exactly what you're looking for:

http://www.sequenceontology.org/miso/current_release/term/SO:0000007

However, if your read pair comes from a different contig, or exists in some
abstract sense, not associated with the assembly of the contig, and you're
just *aligning them to another sequence*, then a match, with (at least) two
match_part children corresponding to the regions that each read matches
could be more appropriate.

Which of these options best reflects your data?

Cheers,

L.



-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
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