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After coming long way through blastn, and all of it's big family, to all kinds of burrows-wheeler aligners, now I'm interested in using HMM for dna alignment. I would use HMMER, but sequences are from PacBio so it's not an option.
Does anyone has any clue how to do it?
Best for me would be advices like:
which module use first (buildmodel I suppose)
Build model on what, query sequence or reference?
How to align (just basics, with no specification, I will deal with it).
Does anyone has any clue how to do it?
Best for me would be advices like:
which module use first (buildmodel I suppose)
Build model on what, query sequence or reference?
How to align (just basics, with no specification, I will deal with it).
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