RE: [Gmod-gbrowse] Seq with filtered blast results?

[Scott C. <ca...@cs...>]

Marc,

That is very cool--thanks much.  It is much more elegant than the hack I
had in my head, so I'm glad I didn't spend much time working on it.  Do
you want to commit this to cvs?  (If you don't want to, I will; if you
don't have an account and want one, let me know.)

Thanks again,
Scott


On Sat, 2004-01-31 at 15:06, Marc Logghe wrote:
> Hi all,
> I've implemented filtering functionality in the Gbrowse cvs build from last night.
> At least the most essential edits have been done in order to show that it works.
> You can try for yourself at my site if you'd like: http://81.164.110.58:4280/cgi-bin/gbrowse.
> Filtering is done using a plugin of new type 'Filter'. The FilterTest plugin filters the ORF track of the yeast genome sample. You can filter for the ORFs on the Watson or Crick strand. It is all about setting a filter configuration option on the fly. Its value is a closure, returning 1 or 0 depending on whether you want to keep the feature or not.
> You can filter on anything. If your filter plugin is acting on EST features for instance, you can check for any attribute e.g. score, length, strand, ... I've set it up so that you also can pass a value via the filter configuration (not used here in the yeast ORF example) so that you can filter on say ESTs with a score better than the passed value.
> In the footer of the page I've set a link to the tarball.
> HTH,
> Marc
> 
> 
>  
> > -----Original Message-----
> > From: Wiepert, Mathieu [mailto:Wie...@ma...]
> > Sent: Thursday, January 29, 2004 8:24 PM
> > To: Gbrowse (E-mail)
> > Subject: [Gmod-gbrowse] Seq with filtered blast results?
> > 
> > 
> > Hi,
> > 
> > I have a simple question I think.  I have a gene, with about 
> > 10kb flanking on either side.  I would like to display that 
> > gene, and all the EST's that align to it with GBrowse, show 
> > alternative splicing, but adjust the alignments shown based 
> > on %ID.  So a default would be something like UCSC, but then 
> > maybe expand the matches shown on the fly (  
> > 
> > UCSC says
> > "When a single EST aligns in multiple places, the alignment 
> > having the highest base identity is found. Only alignments 
> > that have a base identity level within 0.1% of the best are 
> > kept. Alignments must also have at least 98% base identity to 
> > be kept. "
> > 
> > But say I want to show alignments of 95%, that sort of thing. 
> >  Is it easy to do that on the fly, with track options or something?
> > 
> > -mat
> > 
> > 
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         ca...@cs...
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory