[Bioperl-l] Re: GFF3 preliminary

[Aaron J Mackey]

> 3) I'm not convinced by the format for the Align string.  This requires
> a character per aligned base.  There are a variety of run-length type
> encodings in common use that are much more compact.

To add one more, recent FASTA programs provide compact alignment
representations via "60=1-8=3+15=" (Ensembl M is =, D is - and I is +); we
also use / and \ for backwards and forwards frameshifts (which allows easy
intron "gapping").  We find this easier to read then CIGAR format, as the
"glyphs" are less visually distracting, compared to the numbers.

-Aaron

-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey at virginia.edu