[Bioperl-l] Blast to gff

[Lincoln Stein]

> however, I suspect you will find the gff_string a little thin and almost
> certainly not to the taste of what you want to feed it into (eg, Apollo or
> whatever) - GFF is a very... open... standard.

There may soon be a new GFF-family format associated with the sequence 
ontology.  This arises out of discussions with Michael Ashburner, Richard 
Durbin and Suzi Lewis at the recent Standards for Ontologies meeting.  The 
format would be backward compatible with GFF, but the feature type field 
would be constrained, and the attributes column would clearly distinguish 
between ID, group and other attributes.

We also discussed Thomas Down's XFF format, but there still seems to be a 
generalized yearning for an easy to read tab-delimited fallback format that 
is semantically meaningful.  Probably the Philosopher's Stone of 
bioinformatics.

Lincoln

-- 
Lincoln Stein
lstein@cshl.org