How can find conserved domains of protein's sequence offline?

Question

[m.koohi.m]

Dear friends,

I were wondering if there are any tools to predict conserved domain offline? I don't want to use online approach such as ncbi conserve domain prediction.

Thank you

[Pierre Lindenbaum]

how about using the ncbi batch API? http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#BatchRPSBWebAPI_GETorPOST

Answer 1

[Michael]

Yes, you can do a fully local search using CDD. Documentation is here: http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#RPSBFtp

In short:

• download and install Blast including RPS-Blast
• download the CDD blast database
• run RPS-Blast with this database

Alternatively or additionally install and run InterProScan locally.