[BiO BB] Substitution matrices vs HMM

[Goel, Manisha]

Hi All,

I was trying to develop an algorithm for describing/predicting a pattern
(e.g. transmembrane region, signal peptide etc) in protein sequences.
I want to derive this pattern from the multiple sequence alignments. 
But I was wondering if I should use substitution matrices or HMMs to
describe/represent these patterns.
Are there any definite advantages of using one over the other ? Does the
choice depend on what I am trying to define ?
Can somebody please direct me to relevant literature or suggest
something from personal experience ?


Thanks in advance, 
Manisha Goel
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