I have read both the documentation and research articles for HHsuite and HMMER, but in terms of practical usage or tangibility when do individuals in this field prefer to use one of these search methods over the other?
Hi Murphy,
Check this paper
Rapid and enhanced remote homology detection by cascading hidden Markov model searches in sequence space
That does not answer my question as this paper just discusses performance. I am not talking about performance/accuracy.
I'm asking in what practical scenarios would it be better to use one over the other (from people's experience) from other. i.e is one better with longer or shorter sequences? Is JackHMMER better at finding smaller overlapping regions between protein sequences? Also JackHMMER only appears to be available as an online server and not as a downloadable program for linux/unix?
I'm more asking for experienced users to discuss their general experiences with using both programs.
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