SAM HMM DNA alignment

nanto

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Join Date: Sep 2012

Posts: 19
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#1

SAM HMM DNA alignment

10-23-2012, 05:29 AM

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).
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huliang1000

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Join Date: Jun 2013

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#2

06-02-2013, 02:53 AM

Sam hmm

hi
have you got through about SAM HMM, can I ask you some question?
my email: [email protected] ,waiting for your reply
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