Question: how I can use z-score to decide if the results from viterbi are significant or not ?
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gravatar for Tamador
2.6 years ago by
Tamador10
Tamador10 wrote:

I worked with group in project about how we can use hidden Markov model to detect more member of gene family using viterbi algorithm . We construct HMM from DNA aligned sequences and then we used viterbi algorithm to calculate score for query sequence.

My question is how I can use z-score to decide if the results from viterbi are significant or not ? should I calculated the mean and the Standard deviation from aligned sequences ? if yes, how i do that and if no , what I should do ?

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Tamador10
3

I know this is not your question, but the choice to use the Viterbi algorithm for detecting additional members of a gene family strikes me as odd. The "standard" approach would be to use the forward-backward algorithm to calculate the posterior probability of the query sequence given the HMM.

ADD REPLYlink written 2.6 years ago by Lars Juhl Jensen11k

Sorry for the inconvenience , but could you tell me what is the different between viterbi and forward algorithm ??

ADD REPLYlink written 2.6 years ago by Tamador10
3

Ignoring the issue of whether to use the Viterbi or forward-backward algorithm, I would in any case not use z-scores for assessing significance. The relationship between z-score and statistical significance is based on assuming a normal distribution. I would not expect the scores from the Viterbi algorithm to follow the normal distribution; my best guess would be that they follow an extreme value distribution.

ADD REPLYlink written 2.6 years ago by Lars Juhl Jensen11k

Our project was based on the use of viterbi algorithm and z score , that's not my choice

ADD REPLYlink written 2.6 years ago by Tamador10
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What software are you using to construct the HMM? HMMER will take care of most of the issues for you: it will use forward-backward and EVD to estimate the significance.

ADD REPLYlink written 2.6 years ago by lh331k

I did not use any software , we wrote a c++ code to build HMM

ADD REPLYlink written 2.6 years ago by Tamador10
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