TRAL 2.0: Tandem Repeat Detection With Circular Profile Hidden Markov Models and Evolutionary Aligner

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 versio...

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Autores principales: Delucchi, Matteo, Näf, Paulina, Bliven, Spencer, Anisimova, Maria
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Bioinformatics
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9581039/
https://www.ncbi.nlm.nih.gov/pubmed/36303789
http://dx.doi.org/10.3389/fbinf.2021.691865
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author Delucchi, Matteo
Näf, Paulina
Bliven, Spencer
Anisimova, Maria
author_facet Delucchi, Matteo
Näf, Paulina
Bliven, Spencer
Anisimova, Maria
author_sort Delucchi, Matteo
collection PubMed
description 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 via vital-it.ch/software/tral.
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spelling pubmed-95810392022-10-26 TRAL 2.0: Tandem Repeat Detection With Circular Profile Hidden Markov Models and Evolutionary Aligner Delucchi, Matteo Näf, Paulina Bliven, Spencer Anisimova, Maria Front Bioinform Bioinformatics 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 via vital-it.ch/software/tral. Frontiers Media S.A. 2021-06-25 /pmc/articles/PMC9581039/ /pubmed/36303789 http://dx.doi.org/10.3389/fbinf.2021.691865 Text en Copyright © 2021 Delucchi, Näf, Bliven and Anisimova. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Bioinformatics
Delucchi, Matteo
Näf, Paulina
Bliven, Spencer
Anisimova, Maria
TRAL 2.0: Tandem Repeat Detection With Circular Profile Hidden Markov Models and Evolutionary Aligner
title TRAL 2.0: Tandem Repeat Detection With Circular Profile Hidden Markov Models and Evolutionary Aligner
title_full TRAL 2.0: Tandem Repeat Detection With Circular Profile Hidden Markov Models and Evolutionary Aligner
title_fullStr TRAL 2.0: Tandem Repeat Detection With Circular Profile Hidden Markov Models and Evolutionary Aligner
title_full_unstemmed TRAL 2.0: Tandem Repeat Detection With Circular Profile Hidden Markov Models and Evolutionary Aligner
title_short TRAL 2.0: Tandem Repeat Detection With Circular Profile Hidden Markov Models and Evolutionary Aligner
title_sort tral 2.0: tandem repeat detection with circular profile hidden markov models and evolutionary aligner
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9581039/
https://www.ncbi.nlm.nih.gov/pubmed/36303789
http://dx.doi.org/10.3389/fbinf.2021.691865
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