[BiO BB] COGs

[Boris Steipe]

Hm. A simple BLAST will not necessarily find orthologues. Rememeber, 
COGs are not just functional annotations, they are Clusters of 
Orthologous Groups.

Since COGs are produced by the NCBI you will not find them elsewhere, 
if they are not on the NCBI site. You can of course try to emulate 
their procedure of finding reciprocal best-matches.

If you can define more precisely what you are trying to achieve, maybe 
there are alternative ways to do this.


Boris


> Hi
>
> You could do a simple protein blast of
> COG regions -- >  in genome 1 with the other genome.
> You could also subject both the genomes to domain
> analysis and identify /compare domains.
>
> Is there anything specific you are looking for ???
>
> -Govind
> --- "Tucker, James" <j.d.tucker at vla.defra.gsi.gov.uk>
> wrote:
>> Hi All,
>> I'm looking in to regions of differences in 2
>> genomes.
>> In order to help me simplify and understand the
>> information I'm looking at
>> the COG groups that they fall into.
>> However one of the Genomes does not have COGs
>> details on the NCBI site.
>> Can anyone tell me of an alternative  ?
>> I've tried DDBJ but couldn't find any COG details.
>> Thanks in advance for any help.
>> Regards
>> James
>>
>> James Tucker
>> Brucella Research Group
>> Department of Bacterial Diseases
>> VLA Weybridge
>> Woodham Lane
>> New Haw
>> Addlestone
>> Surrey
>> KT15 3NB
>>
>> Tel: ++44(0)1932 357227 / 359595
>> Fax: ++44(0)1932 357873
>>
>> mailto:j.d.tucker at vla.defra.gsi.gov.uk
>>
>>
>>
>>
>>
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---
Boris Steipe
University of Toronto
Program in Proteomics & Bioinformatics
Departments of Biochemistry & Molecular and Medical Genetics
http://biochemistry.utoronto.ca/steipe/