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

Jane Lomax jane at ebi.ac.uk
Tue Oct 31 08:50:36 PST 2006


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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