Multiple Sequence Alignment using Hidden Markov Model (HMM)

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Tanil
Tanil am 8 Apr. 2013
Hi, I am currently trying to get 2 pdb files and perform a sequence alignment between them with the use of hmm algorithm.
Currently I am using the 'getpdb' function to get the residue and from there can obtain the sequence.
I know there are HMM functions that exist but either I do not know how to implement them correctly or they do not work in the way I imagine them to run.
I am comparing the nwalign algorithm with hmm.
Any feedback will be greatly appreciated.
Kind regards,
Tanil Patel

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