There are any way to conduct a motif search with pfam or CDD-NCBI with a big fasta file?

Question

[schlogl]

Hey guys I would like to get a huge fasta file loaded in pfam or any other data base do you have any ideas how could I do that? Or maybe get all the pfam domains to make a local search?

Thank you

Answer 1

[Mensur Dlakic]

I think the best solution for your problem is to download databases and search locally. Here is CDD and you will need rps-blast from the BLAST suite of programs to perform the search.

Latest Pfam version is here, and you will need to download Pfam-A.hmm.gz. HMMer is used for searching.

[psschlogl]

Hey Mensur Thank you for your suggestions. 8)