This is a test version of Biostars. For the public version, visit https://www.biostars.org.
can I buld a HMM for leters not for amino or nucleotides?

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

hmm profile
• 2,123 views • link
written by alejocn5 • alejocn5

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.

• 1 views • link
written by Michael Dondrup Michael Dondrup

1 answer

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)

• 1 views • link
written by alejocn5 • alejocn5

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

• 1 views • link
written by Jean-Karim Heriche Jean-Karim Heriche

Log in to answer this question.

More posts like this