Protein Profile Analysis: an exploration with HMM

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Er. Neeshu Sharma
Er. Dinesh Kumar, Er. Reet Kamal Kaur


HMM has found its application in almost every field. Applying Hmm to biological sequences has its own advantages. HMM’s being more systematic and specific, yield a result better than consensus techniques. Profile HMMs use position specific scoring for the matching & substitution of a residue and for the opening or extension of a gap. HMMs apply a statistical method to estimate the true frequency of a residue at a given position in the alignment from its observed frequency while standard profiles use the observed frequency itself to assign the score for that residue. This means that a profile HMM derived from only 10 to 20 aligned sequences can be of equivalent quality to a standard profile created from 40 to 50 aligned sequences.




Keywords: Sequence Alignment, Profile Analysis, Hmm, Profile HMM.


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