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Old 12-11-2014, 03:32 PM   #1
Antony03
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Default COG categories of protein sequences

Hello,

I have protein sequences and I would like to know the COG category for each sequence. What is the best procedure?

Sincerely,

Antony

Last edited by Antony03; 12-11-2014 at 05:14 PM.
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Old 12-15-2014, 02:41 PM   #2
Antony03
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Please, a little up!
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Old 12-15-2014, 05:31 PM   #3
GenoMax
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See if this thread helps: http://seqanswers.com/forums/showthread.php?t=35035

Are you just looking to map sequences to COG categories or do you want to build COG's from the set you have?
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Old 12-16-2014, 03:38 AM   #4
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Hello GenoMax,

Thank you for your answer. The thread does not really seems helpful for me. I have >1000 sequences in amino acids, is there a way to perform a "blast-like" alignment to get the COG category for each sequence.
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Old 12-16-2014, 03:46 AM   #5
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I had a look at the COGsoft software. I think that should do what you need. You can find the software at this link: ftp://ftp.ncbi.nih.gov/pub/wolf/COGs/COGsoft/. Get the newest release. You can check the README file included in the tarball for additional information and look for the COGnitor program.

You still need to run the blast searches yourself before using COGnitor to assign categories to blast hits.

Last edited by GenoMax; 12-16-2014 at 03:55 AM.
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