JUCHMME: a Java Utility for Class Hidden Markov Models and Extensions for biological sequence analysis

Ioannis A Tamposis; Konstantinos D Tsirigos; Margarita C Theodoropoulou; Panagiota I Kontou; Georgios N Tsaousis; Dimitra Sarantopoulou; Zoi I Litou; Pantelis G Bagos

doi:10.1093/bioinformatics/btz533

JUCHMME: a Java Utility for Class Hidden Markov Models and Extensions for biological sequence analysis

Bioinformatics. 2019 Dec 15;35(24):5309-5312. doi: 10.1093/bioinformatics/btz533.

Authors

Ioannis A Tamposis¹, Konstantinos D Tsirigos², Margarita C Theodoropoulou¹, Panagiota I Kontou¹, Georgios N Tsaousis³, Dimitra Sarantopoulou⁴, Zoi I Litou⁵, Pantelis G Bagos¹

Affiliations

¹ Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece.
² Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kgs Lyngby, Denmark.
³ Department of Bioinformatics, Genekor Medical SA, Athens, Greece.
⁴ Institute of Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA.
⁵ Section of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece.

PMID: 31250907
DOI: 10.1093/bioinformatics/btz533

Abstract

Summary: JUCHMME is an open-source software package designed to fit arbitrary custom Hidden Markov Models (HMMs) with a discrete alphabet of symbols. We incorporate a large collection of standard algorithms for HMMs as well as a number of extensions and evaluate the software on various biological problems. Importantly, the JUCHMME toolkit includes several additional features that allow for easy building and evaluation of custom HMMs, which could be a useful resource for the research community.

Availability and implementation: http://www.compgen.org/tools/juchmme, https://github.com/pbagos/juchmme.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Sequence Analysis
Software*