[GMOD-devel] Re: [Open-bio-l] Schema for genes & features&mappings to assemblies

[Ewan Birney]

On Thu, 2 May 2002, Lincoln Stein wrote:

> The AceDB model for handling gapped alignments might be worth looking
> at.  There is a single Homol_data object to represent the overall
> alignment between two sequences.  The Homol_data object contains the
> details of the alignments of the gapped HSPs.  How similar is this to
> what you're talking about?


This is very similar to the Ensembl "cigar line" system (the cigar line
being an ASCII text representation of the gaps in dense form)