[Bioperl-l] Re: Seq or SeqIO to BSML

[Ewan Birney]

On Fri, 3 Aug 2001, Nathan O. Siemers wrote:

> 
> Hello Ewan,
> 
>         As mentioned, we have volunteered to write a BSML output
>         module for Seq or SeqIO objects, initially for use with
>         ensembl but of course to be designed to be generally useful.  


Basically go for SeqIO system and from there we can put in additional
hooks.

> 
>         Could you provide a data dumper output of a fairly small but
>         richly annotated area of the genome from ensembl?  We can eval
>         it up locally and use it as our starting point.
> 

It is easy to generate -> go to ensembl -> find a gene rich region ->
click on export -> click on generate flat file



>         Finally, I would welcome discussion as to where this code
>         should eventually be placed (how tightly integrated?)  in the
>         bioperl structure.
> 


It should be a SeqIO module, working off RichSeq definitions like
embl/genbank but able to cope with Bio::SeqI stuff. I'll handle any
necessary ensembl extensions first off as it will probably confuse you ;)



>         Thanks,
> 
> 
>         nathan
> 
>         
> 
>         
> 
> -- 
> Nathan Siemers, Group Leader, Bioinformatics-Applied Genomics
> Bristol-Myers Squibb Pharmaceutical Research Institute, Hopewell 3-0.07
> P.O. Box 5400, Princeton, NJ 08543-5400, (609)818-6568
> nathan.siemers@bms.com
> 

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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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