[Gusdev-gusdev] Loading BLAST results

[Arnaud K. <ax...@sa...>]

Hi

I want to load BLAST results in GUS.
Before running LoadBlastSimFast module, I want to load Uniprot and EMBL 
databases in DoTS::ExternalAASequence and DoTS::ExternalNASequence., 
just the Ids not the sequences themselves.

I need some help to use GUS::Common::Plugin::InsertNewExternalSequences 
plugin.

I have the sequences in FASTA, what regexp shall I need  ? Is only  
--regex_name parameter required ? I don't know the taxon attached to the 
sequence entries. Does it matter if I don't give taxon_id parameter ?

Re. LoadBlastSimFast module, It seems to parse the output in a specific 
format. Does it require generateBlastSimilarity.pl script ? Where can I 
get this script ?

cheers
Arnaud

-- 
Arnaud Kerhornou

The Wellcome Trust Sanger Institute
The Pathogen Sequencing Unit
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Work: +44 (0) 1223 494955
Fax: +44 (0) 1223 494919