Re: [Gusdev-gusdev] parseBlastFilesForSimilarity.pl

[Steve F. <sfi...@pc...>]

see below

Alberto Davila wrote:

>We are doing this for Garsa (another system) .. basically we have a
>bioperl parser (Bio::Search::IO) that reads the Blast results file and
>extract all the needed info (to the "Blast_Hit" table)... and also load
>into a given table (eg: External_DB) all the sequences (in fasta format)
>presenting similarity with the queries... at the end we have "Blast_Hit"
>and "External_DB" populated with the same script.
>
>  
>
wow, great.  could you make a gus plugin from that?

>Regarding Interpro and Glimmer, the main problem is to know in which
>tables we should load the parsed results ?
>
>  
>
describe the info you want to store.

steve

>Alberto
>
>On Fri, 2005-02-11 at 13:21 -0500, Y. Thomas Gan wrote:
>  
>
>>I was going to give the same answer steve gave for interpro and gene 
>>finding results.
>>
>>For loading sequences into GUS, the dillema with option 2 is: how do you 
>>know which sequence to load when you load (which is before you actually 
>>have the similarity result)? One solution would be to initially load 
>>complete dataset(s) but delete those without similarity after loading 
>>similarity results.
>>
>>-Thomas
>>
>>On Fri, 11 Feb 2005, Steve Fischer wrote:
>>
>>    
>>
>>>alberto-
>>>
>>>we've never loaded interpro, so there isn't a plugin. 
>>>i believe plasmodb has loaded glimmer results, though i'm not sure.   i have 
>>>asked a plasmodb developer to answer that question.
>>>
>>>steve
>>>
>>>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
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>                            
>>>>>>>>>>>>>>