COG categories of protein sequences

[Antony03]

Hello,

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

Sincerely,

Antony

[Antony03]

Please, a little up!

[GenoMax]

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?

[Antony03]

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.

[GenoMax]

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.