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This article is part of the supplement: The 2007 International Conference on Bioinformatics & Computational Biology (BIOCOMP'07)

Open Access Research

HMMEditor: a visual editing tool for profile hidden Markov model

Jianyong Dai1 and Jianlin Cheng2*

Author Affiliations

1 School of Electrical Engineering and Computer Science, University of Central Florida, Orland, FL 32816, USA

2 Department of Computer Science, Informatics Institute, University of Missouri Columbia, Columbia, MO 65211, USA

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BMC Genomics 2008, 9(Suppl 1):S8  doi:10.1186/1471-2164-9-S1-S8

Published: 20 March 2008

Abstract

Background

Profile 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.

Results

We 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.

Conclusion

HMMEditor 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.