Re: [Gusdev-gusdev] parseBlastFilesForSimilarity.pl

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

Thanks Bindu,

We will have a look on it... also, just found a Bioperl module for
GlimmerM:

http://doc.bioperl.org/bioperl-live/Bio/Tools/Glimmer.html

Cheers, Alberto


On Mon, 2005-02-14 at 14:45 -0500, Bindu Gajria wrote:
> hi Alberto -
> PlasmoDB project uses a plugin to load the GlimmerM results; it is
> GUS::Common::Plugin::ImportPlasmoDBPrediction plugin in the Sanger cvs 
> repository. however, please note that this plugin is not generalized, 
> and has been used here only for the PlasmoDB project so far.
> It would be useful to generalize this plugin some day, so that all can 
> benefit.
> 
> Bindu
> 
> 
> On Feb 11, 2005, at 12:44 PM, Alberto Davila wrote:
> 
> > 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