can I buld a HMM for leters not for amino or nucleotides?

Question

[alejocn5]

hi, I have a question?

How i can Build a HMM profile not for nucleotides to aminoacids, only for letters or words?

thanx a lot

[Michael]

Yes, HMMs can be defined using arbitrary emission symbols and are routinely used in language recognition, but how is this related to bioinformatics then? HMMs are not an invention of bioinformatics.

Answer 1

[alejocn5]

Michael Dondrup thak you for answer

I am using Hmmerscan, but it causes a practical problem , only work whit amino acid or nucleotides, this question is related to bioinformatics because I what to represent another type of elements in the genome, not only (acid or nucleotides) and this elements are more that 24, and i need the complete alphabet to represent this, i look for a program that can generate this and evaluate this profiles in sequence (of the same elements)

[Jean-Karim Heriche]

You can use any generic implementation of HMMs. As a starting point, you can have a look at my HMM perl module here.