Re: [Gusdev-gusdev] parseBlastFilesForSimilarity.pl

[Alberto D. <da...@io...>]

Hey Steve, Thomas,

Thanks a lot for the tips, really helpful.. now, few more questions:

> ok.  NR = NRDB
> 
> the way we have used gus with similarities is that both the query and 
> subject are loaded into gus.  As thomas explained, the similarity table 
> captures similarity between sequences that are in gus. 
> 
> our approach has always been to just load (warehouse) the entire subject 
> database (NR, EST) that we are blasting against.
> 
> the current plugins and blastSimilarity are set up for this.
> 
> obviously, this takes a lot of disk space.  two major efficiencies that 
> we don't currently have plugins for would be:
>   1. to only store in gus a *reference* to the external sequence (ie, 
> don't store the actgs).
>   2. only store in gus the sequences that actually have similarities

Option 2 sound better for us, since we will be blasting against several
databases (> 10GB databases)

What about the plugins to load Interpro and "gene finder" (glimmer, etc)
results ? Is there any at all ?

Cheers, Alberto

> 
> steve
> 
> Alberto Davila wrote:
> 
> >All the blastable databases I mentioned are standard databases from NCBI
> >(ftp://ftp.ncbi.nlm.nih.gov/blast/db/blastdb.txt):
> >
> >NT = nucleotides
> >
> >~30000 entries from genbank (genbank format) are loaded into GUS now.
> >
> >Not sure about your "NRDB", I know NR from NCBI that is a collection of
> >aminoacid entries, could it be the same ?
> >
> >Alberto
> >
> >On Fri, 2005-02-11 at 10:43 -0500, Steve Fischer wrote:
> >  
> >
> >>(what is NT?)
> >>
> >>which of these (genbank, your fasta, NRDB, NT, EST) have you loaded into 
> >>gus?
> >>
> >>steve
> >>
> >>Alberto Davila wrote:
> >>
> >>    
> >>
> >>>Query:
> >>>
> >>>Either sequences from genbank (genbank format) or sequences generated in
> >>>the lab (fasta format)
> >>>
> >>>Blastable databases (all are formatted databases from NCBI):
> >>>
> >>>NR
> >>>NT
> >>>EST
> >>>
> >>>Alberto
> >>>
> >>>On Fri, 2005-02-11 at 10:34 -0500, Steve Fischer wrote:
> >>> 
> >>>
> >>>      
> >>>
> >>>>for the blast, what are the query sequences and what are the blastable 
> >>>>databases?
> >>>>
> >>>>steve
> >>>>
> >>>>Alberto Davila wrote:
> >>>>
> >>>>   
> >>>>
> >>>>        
> >>>>
> >>>>>Basically we will use sequences (loaded into GUS with the GBParser) for
> >>>>>NCBI Blast (Blastx, Blastp and TBlastX), the same sequences will be also
> >>>>>used for Interpro analyses. Results of both (Blast and Interpro) will be
> >>>>>loaded into GUS. We will parse specific things from the Blast results, I
> >>>>>would say:
> >>>>>
> >>>>>`Gi` 
> >>>>>`Accession` 
> >>>>>`Description` 
> >>>>>`E_value` 
> >>>>>`Score` 
> >>>>>`Length` 
> >>>>>`Frame_Query` 
> >>>>>`Frame_Hit` 
> >>>>>`Identical` 
> >>>>>`Hsp_Frac_Identical` 
> >>>>>`Conserved` 
> >>>>>`Hsp_Frac_Conserved`
> >>>>>`Query_Start`
> >>>>>`Query_End` 
> >>>>>`Hit_Start` 
> >>>>>`Hit_End` 
> >>>>>`Hsp_Align` 
> >>>>>`database_letters` 
> >>>>>`database_entries` 
> >>>>>
> >>>>>We already have a Bioperl parser for that (specific for another system:
> >>>>>GARSA) that could be adapted to GUS, problem being we are not sure what
> >>>>>tables should be used to store those data in GUS.
> >>>>>
> >>>>>Cheers, Alberto
> >>>>>
> >>>>>
> >>>>>On Fri, 2005-02-11 at 10:06 -0500, Steve Fischer wrote:
> >>>>>
> >>>>>
> >>>>>     
> >>>>>
> >>>>>          
> >>>>>
> >>>>>>what are you planning on blasting?
> >>>>>>
> >>>>>>steve
> >>>>>>
> >>>>>>Alberto Davila wrote:
> >>>>>>
> >>>>>>  
> >>>>>>
> >>>>>>       
> >>>>>>
> >>>>>>            
> >>>>>>
> >>>>>>>Hi Steve,
> >>>>>>>
> >>>>>>>On Fri, 2005-02-11 at 08:56 -0500, 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?
> >>>>>>>> 
> >>>>>>>>
> >>>>>>>>      
> >>>>>>>>
> >>>>>>>>           
> >>>>>>>>
> >>>>>>>>                
> >>>>>>>>
> >>>>>>>They are not, there would be any howto/tips for that plugin ? We will
> >>>>>>>certainly need a plugin to load "Interpro" and "ORF finding" results
> >>>>>>>into GUS... If they are not available, then maybe we will have to write
> >>>>>>>them ...
> >>>>>>>
> >>>>>>>Cheers, Alberto
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>    
> >>>>>>>
> >>>>>>>         
> >>>>>>>
> >>>>>>>              
> >>>>>>>
> >>>>>>>>steve
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>Poliana Mateus wrote:
> >>>>>>>>
> >>>>>>>> 
> >>>>>>>>
> >>>>>>>>      
> >>>>>>>>
> >>>>>>>>           
> >>>>>>>>
> >>>>>>>>                
> >>>>>>>>
> >>>>>>>>>Hello all,
> >>>>>>>>>
> >>>>>>>>>Where can find the script parseBlastFilesForSimilarity.pl??
> >>>>>>>>>I'm trying to run LoadBlastSimFast...
> >>>>>>>>>
> >>>>>>>>>Poliana
> >>>>>>>>>                  
> >>>>>>>>>
> >
> >  
> >