TRAL 2.0 : tandem repeat detection with circular profile hidden Markov models and evolutionary aligner

Delucchi, Matteo; Näf, Paulina; Bliven, Spencer; Anisimova, Maria

doi:10.3389/fbinf.2021.691865

Please use this identifier to cite or link to this item: https://doi.org/10.21256/zhaw-22764

Publication type:	Article in scientific journal
Type of review:	Peer review (publication)
Title:	TRAL 2.0 : tandem repeat detection with circular profile hidden Markov models and evolutionary aligner
Authors:	Delucchi, Matteo Näf, Paulina Bliven, Spencer Anisimova, Maria
et. al:	No
DOI:	10.3389/fbinf.2021.691865 10.21256/zhaw-22764
Published in:	Frontiers in Bioinformatics
Volume(Issue):	1
Issue:	691865
Issue Date:	25-Jun-2021
Publisher / Ed. Institution:	Frontiers Research Foundation
ISSN:	2673-7647
Language:	English
Subjects:	Bioinformatics; Profile hidden markov models; Computational biology; Genome annotation; Protein sequence analysis; Tandem repeats
Subject (DDC):	004: Computer science 572: Biochemistry
Abstract:	The Tandem Repeat Annotation Library (TRAL) focuses on analyzing tandem repeat units in genomic sequences. TRAL can integrate and harmonize tandem repeat annotations from a large number of external tools, and provides a statistical model for evaluating and filtering the detected repeats. TRAL version 2.0 includes new features such as a module for identifying repeats from circular profile hidden Markov models, a new repeat alignment method based on the progressive Poisson Indel Process, an improved installation procedure and a docker container. TRAL is an open-source Python 3 library and is available, together with documentation and tutorials viavital-it.ch/software/tral.
URI:	https://digitalcollection.zhaw.ch/handle/11475/22764
Fulltext version:	Published version
License (according to publishing contract):	CC BY 4.0: Attribution 4.0 International
Departement:	Life Sciences and Facility Management
Organisational Unit:	Institute of Computational Life Sciences (ICLS)
Published as part of the ZHAW project:	REFRACT – Repeat protein Function, Refinement, Annotation and Classification of Topologies Trans-omic approach to colorectal cancer: an integrative computational and clinical perspective Frequentist estimation of the evolutionary history of sequences with substitutions and indels
Appears in collections:	Publikationen Life Sciences und Facility Management

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Delucchi, M., Näf, P., Bliven, S., & Anisimova, M. (2021). TRAL 2.0 : tandem repeat detection with circular profile hidden Markov models and evolutionary aligner. Frontiers in Bioinformatics, 1(691865). https://doi.org/10.3389/fbinf.2021.691865

Delucchi, M. et al. (2021) ‘TRAL 2.0 : tandem repeat detection with circular profile hidden Markov models and evolutionary aligner’, Frontiers in Bioinformatics, 1(691865). Available at: https://doi.org/10.3389/fbinf.2021.691865.

M. Delucchi, P. Näf, S. Bliven, and M. Anisimova, “TRAL 2.0 : tandem repeat detection with circular profile hidden Markov models and evolutionary aligner,” Frontiers in Bioinformatics, vol. 1, no. 691865, Jun. 2021, doi: 10.3389/fbinf.2021.691865.

DELUCCHI, Matteo, Paulina NÄF, Spencer BLIVEN und Maria ANISIMOVA, 2021. TRAL 2.0 : tandem repeat detection with circular profile hidden Markov models and evolutionary aligner. Frontiers in Bioinformatics. 25 Juni 2021. Bd. 1, Nr. 691865. DOI 10.3389/fbinf.2021.691865

Delucchi, Matteo, Paulina Näf, Spencer Bliven, and Maria Anisimova. 2021. “TRAL 2.0 : Tandem Repeat Detection with Circular Profile Hidden Markov Models and Evolutionary Aligner.” Frontiers in Bioinformatics 1 (691865). https://doi.org/10.3389/fbinf.2021.691865.

Delucchi, Matteo, et al. “TRAL 2.0 : Tandem Repeat Detection with Circular Profile Hidden Markov Models and Evolutionary Aligner.” Frontiers in Bioinformatics, vol. 1, no. 691865, June 2021, https://doi.org/10.3389/fbinf.2021.691865.