Machine Boss: rapid prototyping of bioinformatic automata.

ABSTRACT:

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 sequenc

SUBMITTER: Silvestre-Ryan J 

PROVIDER: S-EPMC8034524 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature