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

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

sequencing blast alignment
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updated by Ram Ram • written by m.koohi.m m.koohi.m

1 answer

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.

• 0 views • link
written by Michael Dondrup Michael Dondrup

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