Starting jackhmmer with an HMM

Question

[Matt LaFave]

Web-based jackhmmer (http://www.ebi.ac.uk/Tools/hmmer/search/jackhmmer) allows the user to use an HMM as input, but command-line jackhmmer (from http://hmmer.org/download.html) appears to only accept a single sequence (or a list of sequences, which appear to be searched in paralllel). Is there a way to force command-line jackhmmer to skip the phmmer-like step & accept an HMM as input?

Answer 1

[Jean-Karim Heriche]

According to the documentation here, it seems jackhmmer can read an HMM as its seq input. This is not however mentioned in the user guide. Otherwise, once jackhmmer has built a profile HMM, it searches just like hmmsearch. So if you already have the HMM, you could also use hmmsearch in an iterative fashion (rebuilding the alignment then HMM with hmmbuild at each iteration).