Re: [Gusdev-gusdev] parseBlastFilesForSimilarity.pl

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

A couple more comments. The"big assumption" (also applies to 
LoadBLATAlignments plugin) might seem restrictive and anti-intuitive (thus 
easily assumed otherwise) at first, and impose more work if you just want 
to experiment with your datasets (which could be heterogenious).

But think about it, this is necessay safeguard to protect data integrity 
in GUS. This is dictated by the foreign key constraints (query sequence 
and subject sequence) on the similarity table. In reality, this forces you 
to think carefully about your datasets (e.g. how to organize if have gene 
trap tags from half a dozen sources, and you want to align them all to the 
genome).

-Thomas

On Fri, 11 Feb 2005, Steve Fischer wrote:

> poliana-
>
> oops, the usage statement for LoadBlastSimFast is out of date.   it should 
> instruct you to use the blastSimilarity command.
>
> LoadBlastSimFast makes a big assumption, that the subject and query sequences 
> are in GUS, and their def. lines have GUS primary keys. 
> Are your sequences already loaded into GUS?
>
> steve
>
>
>
> Poliana Mateus wrote:
>
>> Hello all,
>> 
>> Where can find the script parseBlastFilesForSimilarity.pl??
>> I'm trying to run LoadBlastSimFast...
>> 
>> Poliana
>> 
>> 
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