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Machine Boss: rapid prototyping of bioinformatic automata
MOTIVATION: Many software libraries for using Hidden Markov Models in bioinformatics focus on inference tasks, such as likelihood calculation, parameter-fitting and alignment. However, construction of the state machines can be a laborious task, automation of which would be time-saving and less error...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8034524/ https://www.ncbi.nlm.nih.gov/pubmed/32683444 http://dx.doi.org/10.1093/bioinformatics/btaa633 |
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author | Silvestre-Ryan, Jordi Wang, Yujie Sharma, Mehak Lin, Stephen Shen, Yolanda Dider, Shihab Holmes, Ian |
author_facet | Silvestre-Ryan, Jordi Wang, Yujie Sharma, Mehak Lin, Stephen Shen, Yolanda Dider, Shihab Holmes, Ian |
author_sort | Silvestre-Ryan, Jordi |
collection | PubMed |
description | MOTIVATION: Many software libraries for using Hidden Markov Models in bioinformatics focus on inference tasks, such as likelihood calculation, parameter-fitting and alignment. However, construction of the state machines can be a laborious task, automation of which would be time-saving and less error-prone. RESULTS: We present Machine Boss, a software tool implementing not just inference and parameter-fitting algorithms, but also a set of operations for manipulating and combining automata. The aim is to make prototyping of bioinformatics HMMs as quick and easy as the construction of regular expressions, with one-line ‘recipes’ for many common applications. We report data from several illustrative examples involving protein-to-DNA alignment, DNA data storage and nanopore sequence analysis. AVAILABILITY AND IMPLEMENTATION: Machine Boss is released under the BSD-3 open source license and is available from http://machineboss.org/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-8034524 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-80345242021-04-14 Machine Boss: rapid prototyping of bioinformatic automata Silvestre-Ryan, Jordi Wang, Yujie Sharma, Mehak Lin, Stephen Shen, Yolanda Dider, Shihab Holmes, Ian Bioinformatics Original Papers MOTIVATION: Many software libraries for using Hidden Markov Models in bioinformatics focus on inference tasks, such as likelihood calculation, parameter-fitting and alignment. However, construction of the state machines can be a laborious task, automation of which would be time-saving and less error-prone. RESULTS: We present Machine Boss, a software tool implementing not just inference and parameter-fitting algorithms, but also a set of operations for manipulating and combining automata. The aim is to make prototyping of bioinformatics HMMs as quick and easy as the construction of regular expressions, with one-line ‘recipes’ for many common applications. We report data from several illustrative examples involving protein-to-DNA alignment, DNA data storage and nanopore sequence analysis. AVAILABILITY AND IMPLEMENTATION: Machine Boss is released under the BSD-3 open source license and is available from http://machineboss.org/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2020-07-19 /pmc/articles/PMC8034524/ /pubmed/32683444 http://dx.doi.org/10.1093/bioinformatics/btaa633 Text en © The Author(s) 2020. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Papers Silvestre-Ryan, Jordi Wang, Yujie Sharma, Mehak Lin, Stephen Shen, Yolanda Dider, Shihab Holmes, Ian Machine Boss: rapid prototyping of bioinformatic automata |
title | Machine Boss: rapid prototyping of bioinformatic automata |
title_full | Machine Boss: rapid prototyping of bioinformatic automata |
title_fullStr | Machine Boss: rapid prototyping of bioinformatic automata |
title_full_unstemmed | Machine Boss: rapid prototyping of bioinformatic automata |
title_short | Machine Boss: rapid prototyping of bioinformatic automata |
title_sort | machine boss: rapid prototyping of bioinformatic automata |
topic | Original Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8034524/ https://www.ncbi.nlm.nih.gov/pubmed/32683444 http://dx.doi.org/10.1093/bioinformatics/btaa633 |
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