Re: [Gusdev-gusdev] LoadBLATAlignment

[Y. T. G. <yon...@pc...>]

Hi Mark,
The short answer is: yes we *did* have a plugin 
CalculateGeneFeatureSeqOverlaps.pm. I do not know why but it (and also a 
CalculateGeneFeatureESTOverlaps.pm plugin) is now in our legacy cvs repository.
Probably we did not think the plugin is of general interest so we did not 
include it in public release.

Here is how I found it out in our GUS instance and it is a great example 
of how you use the tracking capabilities of GUS.

1) find out if anything is in dots.GeneFeatureSeqOverlap
2) find out who populated it with what algorithm invocations for what 
projects (in this case Jonathan Schug had one run for GUS project, 
Jonathan Crabtree, who is no longer at CBIL, had 4 runs each for GUS 
project and Plasmodium-4.0 project)
3) find out the algorithm implementation id(s) for by 
row_alg_invocation_id
4) find out the algorithm id(s) for the algorithm implementation id(s)
5) find the algorithm name(s) by id

-Thomas

On Wed, 30 Mar 2005, Mark S. Heiges wrote:

>
> I loaded some est BLAT alignments dots.blatalignment with LoadBLATAlignment 
> (ver 1.32) (how many times can I write blat alignment in one sentence?).
>
> My dots.GeneFeatureSeqOverlap table  is empty and I'm thinking there should 
> be data there because it's a child of blatalignment, PlasmoDB uses it and 
> GFSO looks more usable than BA for finding est/gene overlaps. Although, since 
> I aligned ests against whole contigs instead of individual sequences maybe 
> GFSO won't help me.
>
> Is there a plugin to populate GFSO?
>
> Thanks,
> Mark
>
>
>
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