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Generic GO Slims file is missing GOids compared to most recent fasta flat file

Stefan Goetz stefang at fis.upv.es
Tue Oct 31 09:52:16 PST 2006


Hi Jessica, 
Blast2GO will surely help you with that. You can import Blast Results in
XML format or import you generated TOP-Blast GO-Annotations directly
(or, of course generate new B2G annotation :-)). Than you can use all
the functionality B2G offers like the GOSlim functionality,
"Multilevel-Pies" or "GO-Mutiple-Graphs" could be a good way too. Have a
look at the new tutorial of B2G for importing Blast or Annotation Data
into B2G (section 8 (Importing Annotation and Modulate Annotation
Intensity by GOSLIM)) and section 11. Analysis -> A. Descriptive
analysis).
Tutorial: http://www.blast2go.de/b2gdata/blast2goTutorial.pdf
Best regards, 
Stefan Götz

 ------------------------------------------------------------
 | Stefan Götz - stefang(at)fis.upv.es                      |
 | IBM - Biomedical Informatics, Bioinformatics Area        |
 | BET - Bioengineering, Electronics and Telemedicine Group |
 | UPV - Politechnical University of Valencia - Spain       |
 ------------------------------------------------------------ 


> -----Original Message-----
> From: owner-gofriends at genome.stanford.edu 
> [mailto:owner-gofriends at genome.stanford.edu] On Behalf Of Jane Lomax
> Sent: Tuesday, October 31, 2006 5:51 PM
> To: gofriends at genome.stanford.edu
> Cc: Jessica Whitley
> Subject: Fwd: Generic GO Slims file is missing GOids compared 
> to most recent fasta flat file
> 
> 
> Hi - can anyone help Jessica? She wants to find the GO slim  
> categories for a large (22,000) set of GO ids (not in gene  
> association file format, so she can't use map2slim). Does 
> anyone know  
> of/develop any software that can do this?
> 
> thanks,
> 
> Jane
> 
> > On Oct 11, 2006, at 6:51 AM, Jessica Whitley wrote:
> >
> >
> >> Thank you, I believe the ontology file will work for what I am  
> >> trying to do.
> >> I'm aware there is software available to do the GoSLIMS.  
> >> Unfortunately I do
> >> not have the correct type of input file to run it.  Since I am  
> >> trying to get
> >> the GO associations for 22,000 sequences all at once I ran 
> a BLAST  
> >> locally
> >> against the GO database.  This of course only provided me with  
> >> blast results
> >> and not the Associations file that the map2slim.pl program  
> >> requires.  So I
> >> simple wrote a PERL script that would take the BLAST 
> results file,  
> >> extract
> >> the GO numbers for the top results for each sequence and 
> then iterate
> >> through the SLIMS file to find the highest category each sequence  
> >> is in.  If
> >> I use the ontology in place of the SLIMS I think it will 
> work.  Do  
> >> you know
> >> if there might be any other programs that would allow me to go  
> >> from those
> >> blast results to general SLIMS categories?
> >>
> >> Thank you for your help,
> >> Jessica
> >>
> >> -----Original Message-----
> >> From: Mike Cherry [mailto:cherry at stanford.edu]
> >> Sent: Tuesday, October 10, 2006 5:02 PM
> >> To: Jessica Whitley
> >> Cc: gohelp at genome.stanford.edu; Amelia Ireland
> >> Subject: Re: Generic GO Slims file is missing GOids compared to  
> >> most recent
> >> fasta flat file
> >>
> >> Jessica,
> >>
> >> The headers in the files at the URLs below indicate the files are
> >> from October 2006.  I cannot find one that says May?  I'm not sure
> >> why you are seeing something different?
> >>
> >> The purpose of the GO slim files is to provide a subset of 
> the terms
> >> from the ontologies.  These are often used to make pie charts.  The
> >> full ontologies contain all the GO terms.  Those nodes 
> that are part
> >> of the GO slims are indicated within the OBO ontology files.
> >> Software exists that can map a GO ID up to the closest GO 
> slim term.
> >>
> >> The OBO file containing the ontology is available from this
> >> directory, the file name is gene_ontology.obo:
> >>
> >>     http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/ontology/
> >>
> >>
> >>
> >>
> >> On Oct 10, 2006, at 1:41 PM, Jessica Whitley wrote:
> >>
> >>
> >>> That is the file that I pulled down before, apparently 
> the May 2006
> >>> date at
> >>> the top is not updated. The file does not have some of the GO
> >>> numbers I am
> >>> getting after blasting my sequences against the GO database. For
> >>> example:
> >>> GO:0045045 "secretory pathway"
> >>> GO:0004014 "adenosylmethionine decarboxylase activity"
> >>> Do you have any idea why this might be?
> >>>
> >>> Jessica
> >>>
> >>> -----Original Message-----
> >>> From: Mike Cherry [mailto:cherry at stanford.edu]
> >>> Sent: Friday, October 06, 2006 4:41 PM
> >>> To: Jessica Whitley
> >>> Cc: gohelp at genome.stanford.edu
> >>> Subject: Re: Generic GO Slims file is missing GOids compared to
> >>> most recent
> >>> fasta flat file
> >>>
> >>> Jessica,
> >>>
> >>> Sorry you are having trouble with the GO slim.  Please 
> check that  
> >>> you
> >>> retrieve them from either of these two sites:
> >>>
> >>>    ftp://ftp.geneontology.org/pub/go/GO_slims/
> >>>
> >>>    http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/GO_slims/
> >>>
> >>> The GO slims are updated daily.
> >>>
> >>> -Mike
> >>>
> >>>
> >>> On Oct 6, 2006, at 1:33 PM, Jessica Whitley wrote:
> >>>
> >>>
> >>>> The most recent generic slims file is from May 2006, whereas the
> >>>> most recent GO fasta flat file is from September 2006.  When I
> >>>> blast my sequences against the info in the fasta file I 
> get results
> >>>> with GO numbers that are not in the Slims file.  Is this 
> because of
> >>>> the difference in the dates?  Or do the slims files typically not
> >>>> contain references for some GO numbers.
> >>>>
> >>>>
> >>>>
> >>>> Jessica Whitley
> >>>>
> >>>>
> >
> 
> 
> --
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> 



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