Publication Date:
2020-07-19
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/.
Print ISSN:
1367-4803
Electronic ISSN:
1460-2059
Topics:
Biology
,
Computer Science
,
Medicine
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