How to make best guest of protein class from protein sequence

[ajing]

Hi,

I am not quit sure what the best way is to predict the name of protein class (e.g. Oxidoreductases) from protein sequence. Just Blast to the whole PDB and read some attributes of the result? Or very efficient way in biopython or other bioinformatics platform?

[GenoMax]

If you doing this for a small number of sequences then that would be acceptable. How many are you looking at analyzing?

You can download the NCBI CDD database and do the searches locally if you have a large number of sequences: ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/

[ajing]

If you doing this for a small number of sequences then that would be acceptable. How many are you looking at analyzing?

You can download the NCBI CDD database and do the searches locally if you have a large number of sequences: ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/

Thanks GenoMax,

Yes, CD-Search can help. I have thousands of sequence to search, so I want the process to be highly automatic. Could I ask an extented question? How could you find all related term for that protein after you search CDD database.

[rhinoceros]

Thanks GenoMax,

Yes, CD-Search can help. I have thousands of sequence to search, so I want the process to be highly automatic. Could I ask an extented question? How could you find all related term for that protein after you search CDD database.

Consider blasting against the m5nr database. They should update it very soon..