TRAL: tandem repeat annotation library.
Détails
Etat: Public
Version: Final published version
Licence: Non spécifiée
It was possible to publish this article open access thanks to a Swiss National Licence with the publisher.
ID Serval
serval:BIB_968BCDD6E6EF
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Institution
Titre
TRAL: tandem repeat annotation library.
Périodique
Bioinformatics
ISSN
1367-4811 (Electronic)
ISSN-L
1367-4803
Statut éditorial
Publié
Date de publication
2015
Peer-reviewed
Oui
Volume
31
Numéro
18
Pages
3051-3053
Langue
anglais
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov'tPublication Status: ppublish
Résumé
MOTIVATION: Currently, more than 40 sequence tandem repeat detectors are published, providing heterogeneous, partly complementary, partly conflicting results.
RESULTS: We present TRAL, a tandem repeat annotation library that allows running and parsing of various detection outputs, clustering of redundant or overlapping annotations, several statistical frameworks for filtering false positive annotations, and importantly a tandem repeat annotation and refinement module based on circular profile hidden Markov models (cpHMMs). Using TRAL, we evaluated the performance of a multi-step tandem repeat annotation workflow on 547 085 sequences in UniProtKB/Swiss-Prot. The researcher can use these results to predict run-times for specific datasets, and to choose annotation complexity accordingly.
AVAILABILITY AND IMPLEMENTATION: TRAL is an open-source Python 3 library and is available, together with documentation and tutorials via http://www.vital-it.ch/software/tral.
CONTACT: elke.schaper@isb-sib.ch.
RESULTS: We present TRAL, a tandem repeat annotation library that allows running and parsing of various detection outputs, clustering of redundant or overlapping annotations, several statistical frameworks for filtering false positive annotations, and importantly a tandem repeat annotation and refinement module based on circular profile hidden Markov models (cpHMMs). Using TRAL, we evaluated the performance of a multi-step tandem repeat annotation workflow on 547 085 sequences in UniProtKB/Swiss-Prot. The researcher can use these results to predict run-times for specific datasets, and to choose annotation complexity accordingly.
AVAILABILITY AND IMPLEMENTATION: TRAL is an open-source Python 3 library and is available, together with documentation and tutorials via http://www.vital-it.ch/software/tral.
CONTACT: elke.schaper@isb-sib.ch.
Mots-clé
Amino Acid Sequence, Cluster Analysis, Databases, Protein, Documentation, Gene Library, Humans, Knowledge Bases, Molecular Sequence Annotation, Molecular Sequence Data, Software, Tandem Repeat Sequences/genetics
Pubmed
Web of science
Open Access
Oui
Création de la notice
14/04/2016 18:07
Dernière modification de la notice
14/02/2022 8:56
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