Keith Boroevich | 20 Nov 19:43 2008
Picon

BLAST data representation in Chado

Hi all,

I was just looking though the wiki files for chado implementations on 
the gmod site (been a while since I visited it) and I noticed some 
inconsistencies between the way the "Load_BLAST_Into_Chado" program 
represents a BLAST result and the way I thought was correct.

On both http://gmod.org/wiki/Load_BLAST_Into_Chado and 
http://gmod.org/wiki/Chado_Best_Practices#Results_from_BLAST it states 
that an Hit to query featureloc will have a rank of 0 and the Hit to 
target featureloc will have a rank of 0.  However, it also says that the 
HSP to query featureloc will have a rank of 1.  I don't understand the 
latter statement.  What is the purpose of increasing the rank of the HSP 
featureloc and if the HSP to query featureloc is rank 1 what is the rank 
of the HSP to target featureloc?

I always assumed (and implemented) for BLAST that all featurelocs to the 
query were rank 0 and all featurelocs to the target were rank 1.

Thanks in advance.

Keith Boroevich

-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/

Gmane