[Bioperl-l] How to retrieve info about sequence-tagged-sites

[Alice Lu]

Hi Heikki,

I am not aware of other STS interfaces at the moment, but I'll do some
research next week. Also I'll start looking into the Bio::MapIO module,
I am NEW to Bioperl, but this seems to be a good opportunity to combine
learning and making something useful for everybody. 


Alice 
 
 

-----Original Message-----
From: Heikki Lehvaslaiho [mailto:heikki@ebi.ac.uk] 
Sent: Thursday, October 24, 2002 12:50 PM
To: Alice Lu
Cc: bioperl-l@bioperl.org; Hilmar Lapp
Subject: RE: [Bioperl-l] How to retrieve info about
sequence-tagged-sites

Alice,

I am afraid there is nothing in BioPerl for accessing UniSTS. We have a
fairly generic set of objects in Bio::Map namespace and a parser for
mapmaker format but nothing more useful. 

I know that Hilmar Lapp has been thinking about maps and markers in the
context of BioSQL project so maybe something will happen in near future.
Would you be interested in helping to write something?

I certainly am interested in helping to get somethin going on. The
deCode human map places many old polymorphic markers into sequence for
the first time.

I have not used UniSTS, but it really seems to be resource worth
integrating into BioPerl. One problem is that according the front page
the web interface is Entrez which is quite difficult to work with. Is
there a simpler interface to these data?

The first thing would be to write a parser, Bio::MapIO::unists, that can
handle the format. 

	-Heikki

P.S. UniSTS home page: http://www.ncbi.nlm.nih.gov/genome/sts