HMMEditor: a visual editing tool for profile hidden Markov model

<p<Abstract</p< <p<Background</p< <p<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 predic...
Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Cheng Jianlin [verfasserIn] Dai Jianyong [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2008

Übergeordnetes Werk:	In: BMC Genomics - BMC, 2003, 9(2008), Suppl 1, p S8
Übergeordnetes Werk:	volume:9 ; year:2008 ; number:Suppl 1, p S8

Links:	Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1186/1471-2164-9-S1-S8

Katalog-ID:	DOAJ044729871

Internformat


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520			\|a <p<Abstract</p< <p<Background</p< <p<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.</p< <p<Results</p< <p<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.</p< <p<Conclusion</p< <p<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.</p<
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author_variant	c j cj d j dj
matchkey_str	article:14712164:2008----::meioaiuldtntofrrflh
hierarchy_sort_str	2008
callnumber-subject-code	TP
publishDate	2008
allfields	10.1186/1471-2164-9-S1-S8 doi (DE-627)DOAJ044729871 (DE-599)DOAJ0367fc29ea2a4d4ab0fc70f8c4d5b7b6 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Cheng Jianlin verfasserin aut HMMEditor: a visual editing tool for profile hidden Markov model 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<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.</p< <p<Results</p< <p<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.</p< <p<Conclusion</p< <p<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.</p< Biotechnology Genetics Dai Jianyong verfasserin aut In BMC Genomics BMC, 2003 9(2008), Suppl 1, p S8 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:9 year:2008 number:Suppl 1, p S8 https://doi.org/10.1186/1471-2164-9-S1-S8 kostenfrei https://doaj.org/article/0367fc29ea2a4d4ab0fc70f8c4d5b7b6 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2008 Suppl 1, p S8
spelling	10.1186/1471-2164-9-S1-S8 doi (DE-627)DOAJ044729871 (DE-599)DOAJ0367fc29ea2a4d4ab0fc70f8c4d5b7b6 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Cheng Jianlin verfasserin aut HMMEditor: a visual editing tool for profile hidden Markov model 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<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.</p< <p<Results</p< <p<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.</p< <p<Conclusion</p< <p<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.</p< Biotechnology Genetics Dai Jianyong verfasserin aut In BMC Genomics BMC, 2003 9(2008), Suppl 1, p S8 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:9 year:2008 number:Suppl 1, p S8 https://doi.org/10.1186/1471-2164-9-S1-S8 kostenfrei https://doaj.org/article/0367fc29ea2a4d4ab0fc70f8c4d5b7b6 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2008 Suppl 1, p S8
allfields_unstemmed	10.1186/1471-2164-9-S1-S8 doi (DE-627)DOAJ044729871 (DE-599)DOAJ0367fc29ea2a4d4ab0fc70f8c4d5b7b6 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Cheng Jianlin verfasserin aut HMMEditor: a visual editing tool for profile hidden Markov model 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<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.</p< <p<Results</p< <p<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.</p< <p<Conclusion</p< <p<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.</p< Biotechnology Genetics Dai Jianyong verfasserin aut In BMC Genomics BMC, 2003 9(2008), Suppl 1, p S8 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:9 year:2008 number:Suppl 1, p S8 https://doi.org/10.1186/1471-2164-9-S1-S8 kostenfrei https://doaj.org/article/0367fc29ea2a4d4ab0fc70f8c4d5b7b6 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2008 Suppl 1, p S8
allfieldsGer	10.1186/1471-2164-9-S1-S8 doi (DE-627)DOAJ044729871 (DE-599)DOAJ0367fc29ea2a4d4ab0fc70f8c4d5b7b6 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Cheng Jianlin verfasserin aut HMMEditor: a visual editing tool for profile hidden Markov model 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<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.</p< <p<Results</p< <p<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.</p< <p<Conclusion</p< <p<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.</p< Biotechnology Genetics Dai Jianyong verfasserin aut In BMC Genomics BMC, 2003 9(2008), Suppl 1, p S8 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:9 year:2008 number:Suppl 1, p S8 https://doi.org/10.1186/1471-2164-9-S1-S8 kostenfrei https://doaj.org/article/0367fc29ea2a4d4ab0fc70f8c4d5b7b6 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2008 Suppl 1, p S8
allfieldsSound	10.1186/1471-2164-9-S1-S8 doi (DE-627)DOAJ044729871 (DE-599)DOAJ0367fc29ea2a4d4ab0fc70f8c4d5b7b6 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Cheng Jianlin verfasserin aut HMMEditor: a visual editing tool for profile hidden Markov model 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<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.</p< <p<Results</p< <p<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.</p< <p<Conclusion</p< <p<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.</p< Biotechnology Genetics Dai Jianyong verfasserin aut In BMC Genomics BMC, 2003 9(2008), Suppl 1, p S8 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:9 year:2008 number:Suppl 1, p S8 https://doi.org/10.1186/1471-2164-9-S1-S8 kostenfrei https://doaj.org/article/0367fc29ea2a4d4ab0fc70f8c4d5b7b6 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2008 Suppl 1, p S8
language	English
source	In BMC Genomics 9(2008), Suppl 1, p S8 volume:9 year:2008 number:Suppl 1, p S8
sourceStr	In BMC Genomics 9(2008), Suppl 1, p S8 volume:9 year:2008 number:Suppl 1, p S8
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authorswithroles_txt_mv	Cheng Jianlin @@aut@@ Dai Jianyong @@aut@@
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callnumber-first	T - Technology
author	Cheng Jianlin
spellingShingle	Cheng Jianlin misc TP248.13-248.65 misc QH426-470 misc Biotechnology misc Genetics HMMEditor: a visual editing tool for profile hidden Markov model
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topic_title	TP248.13-248.65 QH426-470 HMMEditor: a visual editing tool for profile hidden Markov model
topic	misc TP248.13-248.65 misc QH426-470 misc Biotechnology misc Genetics
topic_unstemmed	misc TP248.13-248.65 misc QH426-470 misc Biotechnology misc Genetics
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title	HMMEditor: a visual editing tool for profile hidden Markov model
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title_full	HMMEditor: a visual editing tool for profile hidden Markov model
author_sort	Cheng Jianlin
journal	BMC Genomics
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lang_code	eng
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contenttype_str_mv	txt
author_browse	Cheng Jianlin Dai Jianyong
container_volume	9
class	TP248.13-248.65 QH426-470
format_se	Elektronische Aufsätze
author-letter	Cheng Jianlin
doi_str_mv	10.1186/1471-2164-9-S1-S8
author2-role	verfasserin
title_sort	hmmeditor: a visual editing tool for profile hidden markov model
callnumber	TP248.13-248.65
title_auth	HMMEditor: a visual editing tool for profile hidden Markov model
abstract	<p<Abstract</p< <p<Background</p< <p<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.</p< <p<Results</p< <p<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.</p< <p<Conclusion</p< <p<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.</p<
abstractGer	<p<Abstract</p< <p<Background</p< <p<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.</p< <p<Results</p< <p<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.</p< <p<Conclusion</p< <p<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.</p<
abstract_unstemmed	<p<Abstract</p< <p<Background</p< <p<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.</p< <p<Results</p< <p<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.</p< <p<Conclusion</p< <p<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.</p<
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container_issue	Suppl 1, p S8
title_short	HMMEditor: a visual editing tool for profile hidden Markov model
url	https://doi.org/10.1186/1471-2164-9-S1-S8 https://doaj.org/article/0367fc29ea2a4d4ab0fc70f8c4d5b7b6 https://doaj.org/toc/1471-2164
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up_date	2024-07-04T00:15:37.394Z
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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.</p< <p<Results</p< <p<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.</p< <p<Conclusion</p< <p<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. 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HMMEditor: a visual editing tool for profile hidden Markov model

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