What are regions for? (was Re: [DAS2] DAS intro)

[Ed Erwin]

Andrew Dalke wrote:
> My questions, to summarize, are:
>   - why do we need a /region space when we can
>       1. point directly to a sequence (for chromosome regions) and/or
>       2. point to a "contig" or "assembly" or "region" feature type
>               (for other regions)

The way I understand it, that is what region is for: to point directly 
to a location on a sequence and/or contig.

>   - When would someone have regions which have more than one of
>      contigs, ESTs and chromosomes?  Especially given that this
>      is the genome spec, so chromosome-level info is known, at
>      least enough for a rough assembly.

I think they do it mainly 1) when the assembly is incomplete or 2) to 
preserve annotations from the past when the assembly was incomplete. 
There could be more reasons.

Here is an example of a DAS/1 server that contains both chromosomes and 
"other" short sequences as entry points:

http://servlet.sanger.ac.uk:8080/das/ensembl_Homo_sapiens_core_28_35a/entry_points

See here for some more genomes that are treated similarly:

http://servlet.sanger.ac.uk:8080/das


> In other words, what are regions for?
> 
>                     Andrew
>                     dalke at dalkescientific.com
> 
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