Title |
HMMEditor: a visual editing tool for profile hidden Markov model
|
---|---|
Published in |
BMC Genomics, March 2008
|
DOI | 10.1186/1471-2164-9-s1-s8 |
Pubmed ID | |
Authors |
Jianyong Dai, Jianlin Cheng |
Abstract |
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. 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. 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. |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Germany | 3 | 6% |
United Kingdom | 3 | 6% |
Colombia | 1 | 2% |
Australia | 1 | 2% |
India | 1 | 2% |
Brazil | 1 | 2% |
Denmark | 1 | 2% |
United States | 1 | 2% |
Unknown | 42 | 78% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 15 | 28% |
Student > Master | 12 | 22% |
Student > Ph. D. Student | 11 | 20% |
Student > Doctoral Student | 3 | 6% |
Other | 3 | 6% |
Other | 8 | 15% |
Unknown | 2 | 4% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 27 | 50% |
Computer Science | 15 | 28% |
Biochemistry, Genetics and Molecular Biology | 2 | 4% |
Engineering | 2 | 4% |
Environmental Science | 1 | 2% |
Other | 3 | 6% |
Unknown | 4 | 7% |