[BioPython] scop

[Jeffrey Chang]

On Tue, 20 Jun 2000, Steve A. Chervitz wrote:

> Cayte wrote:
> 
> >    Browsing through the SCOP database, I don't see dom, lin or
> > location files, that the SCOP parser leads me to expect.  The site has
> > web pages that are roughly like the lin files.  If I look at the HTML
> > source, it contains text, that resembles location and dom.  But I'm
> > not seeing files that I can feed directly into the
> > parser?
> > Cayte
> 
> Try these URLs for the dom and lin files:
> 
> http://scop.berkeley.edu/search.cgi?dir=dom
> http://scop.berkeley.edu/search.cgi?dir=lin

Yes.  Sorry about that.  This should be documented somewhere.

> 
> The dom file is about 1Mb, the lin file is about  7X that size.
> 
> A while back I wrote a bioperl module for working with SCOP data (not
> yet contributed, but
> possibly soon). It might be useful to compare notes.

Yes, that would be nice.  The biopython sources are available in the CVS
tree.  As I recall, the sequence locations in SCOP were not trivial to
parse.

Jeff


> 
> Steve
> 
> 
> 
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