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Scaning A Genome With Simple Markov Model To Find A Motif

Hello, is there some program or function (python, R, perl) that would allow fast scanning of a genome for a motif defined as Markov model (1st or higher order)? I guess this would be more specific than using just PWM. Any guidance is apperciated. Ivo

motif
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written by Kubak • Kubak

It seems that fimo (from MEME) needs a PWM, not a Markov model...

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written by alteralex • alteralex

Why does it need to be a Hidden Markov Model?

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written by Zev.Kronenberg Zev.Kronenberg

I would like to see increase specificity by including dependence between following nucleotides. In fact I do not want a HMM algoritmus. I just want to express set of motifs like MM and than scan sequence with this profile. It is easy to program even for biologist in python, but it is prohibitively slow. Maybe there is a software for this that uses C,... I could not find any soft using MM as profile, only PWM...

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written by Kubak • Kubak

I would just need to fast algorithm than slides over the sequence and evaluates match to markov model. Is it somehow possible to modify existingjavascript:document.forms["comment-form"].submit() HMM libraries (like that there is only one hidden mode)? The speed is my main concern, I would run the scan across plant genome.

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written by Kubak • Kubak

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