Abstract
BackgroundProfile Hidden Markov Model (HMM) is a powerful statistical model to represent a family of DNA, RNA, and protein sequences. Profile HMM has been widely used in bioinformatics research such as sequence alignment, gene structure prediction, motif identification, protein structure prediction, and biological database search. However, few comprehensive, visual editing tools for profile HMM are publicly available.ResultsWe develop a visual editor for profile Hidden Markov Models (HMMEditor). HMMEditor can visualize the profile HMM architecture, transition probabilities, and emission probabilities. Moreover, it provides functions to edit and save HMM and parameters. Furthermore, HMMEditor allows users to align a sequence against the profile HMM and to visualize the corresponding Viterbi path.ConclusionHMMEditor provides a set of unique functions to visualize and edit a profile HMM. It is a useful tool for biological sequence analysis and modeling. Both HMMEditor software and web service are freely available.
Highlights
Profile Hidden Markov Model (HMM) is a powerful statistical model to represent a family of DNA, RNA, and protein sequences
Hidden Markov Model (HMM) is a widely used statistical model for biological sequence analysis [1,2,3,4,5,6]. It has been used in many bioinformatics areas such as motif identification [5,6], gene structure prediction [7], multiple sequence alignment [1,2,3,4], profile-profile alignment [8,9], protein sequence database search [1,3], protein fold recognition [1,3,9], and protein and gene family modeling [1,2,3,4]
At first, we briefly introduce profile Hidden Markov Model generated by HMMer
Summary
At first, we briefly introduce profile Hidden Markov Model generated by HMMer. Another interesting feature of the profile HMM is that there is a transition from B to each M state, and a transition from each M state directly to E state These transitions make it possible to match only a part of the model against a sequence, allowing local alignment with respect to the HMM. HMM visualization Once a profile HMM is loaded, HMMEditor is able to visualize it in the traditional layout view (Figure 2), HMM Logo view and HMM text view It can visualize the corresponding null model. 2. HMM editing HMMer saves a profile HMM model into a text file, in which all the probabilities are converted into log-odds scores. A narrow stack of a matching state means that the state is likely to be deleted instead of being visited in a path
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