Running High-Throughput Searches Using Wise2 Software

Question

[Anand Rao]

Hi all,

I want to search an entire genome using a protein profile HMM as query. I understand that WISE2 was designed to do this, but using heuristics. I have been successful at running genewise and estwise on my local machine. However, I have been unable to complete my installation of WISE2 that can perform HMM versus full genome search because it seems to need certain components for the heuristics based perl programs halfwise.pl and blastwise.pl to work. Do you know how I can have a local version that can perform such a highthrouput search versus an entire genome? (I am interested in hits to more than just protein genes, hence my wish to use WISE2) - but I am not partial to WISE2, any software that can do this, is good enough for me.

Thanks in advance,

Andy R.

Answer 1

[DG]

Are you expecting to try and find unidentified genes which is why you want to scan more than just ESTs and ORFs?

You could combine HMMER3 with doing some sort of rough 6-frame translation of your genomic data but depending on your genome this could get really messy really fast.

Answer 2

[Bert Overduin]

Did you have a thorough look at the Wise2 documentation? If so, and it doesn't answer your question, I suggest you mail Ewan Birney ([e-mail]).