TSEBRA: transcript selector for BRAKER

Abstract Background BRAKER is a suite of automatic pipelines, BRAKER1 and BRAKER2, for the accurate annotation of protein-coding genes in eukaryotic genomes. Each pipeline trains statistical models of protein-coding genes based on provided evidence and, then predicts protein-coding genes in genomic...

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Autores principales:	Lars Gabriel, Katharina J. Hoff, Tomáš Brůna, Mark Borodovsky, Mario Stanke
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Genome annotation Gene prediction Protein-coding genes Evidence integration RNA-seq Protein homology Computer applications to medicine. Medical informatics R858-859.7 Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/c79f7efdc41e45889aec4d525a2a106e
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spelling	oai:doaj.org-article:c79f7efdc41e45889aec4d525a2a106e2021-11-28T12:11:03ZTSEBRA: transcript selector for BRAKER10.1186/s12859-021-04482-01471-2105https://doaj.org/article/c79f7efdc41e45889aec4d525a2a106e2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12859-021-04482-0https://doaj.org/toc/1471-2105Abstract Background BRAKER is a suite of automatic pipelines, BRAKER1 and BRAKER2, for the accurate annotation of protein-coding genes in eukaryotic genomes. Each pipeline trains statistical models of protein-coding genes based on provided evidence and, then predicts protein-coding genes in genomic sequences using both the extrinsic evidence and statistical models. For training and prediction, BRAKER1 and BRAKER2 incorporate complementary extrinsic evidence: BRAKER1 uses only RNA-seq data while BRAKER2 uses only a database of cross-species proteins. The BRAKER suite has so far not been able to reliably exceed the accuracy of BRAKER1 and BRAKER2 when incorporating both types of evidence simultaneously. Currently, for a novel genome project where both RNA-seq and protein data are available, the best option is to run both pipelines independently, and to pick one, likely better output. Therefore, one or another type of the extrinsic evidence would remain unexploited. Results We present TSEBRA, a software that selects gene predictions (transcripts) from the sets generated by BRAKER1 and BRAKER2. TSEBRA uses a set of rules to compare scores of overlapping transcripts based on their support by RNA-seq and homologous protein evidence. We show in computational experiments on genomes of 11 species that TSEBRA achieves higher accuracy than either BRAKER1 or BRAKER2 running alone and that TSEBRA compares favorably with the combiner tool EVidenceModeler. Conclusion TSEBRA is an easy-to-use and fast software tool. It can be used in concert with the BRAKER pipeline to generate a gene prediction set supported by both RNA-seq and homologous protein evidence.Lars GabrielKatharina J. HoffTomáš BrůnaMark BorodovskyMario StankeBMCarticleGenome annotationGene predictionProtein-coding genesEvidence integrationRNA-seqProtein homologyComputer applications to medicine. Medical informaticsR858-859.7Biology (General)QH301-705.5ENBMC Bioinformatics, Vol 22, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Genome annotation Gene prediction Protein-coding genes Evidence integration RNA-seq Protein homology Computer applications to medicine. Medical informatics R858-859.7 Biology (General) QH301-705.5
spellingShingle	Genome annotation Gene prediction Protein-coding genes Evidence integration RNA-seq Protein homology Computer applications to medicine. Medical informatics R858-859.7 Biology (General) QH301-705.5 Lars Gabriel Katharina J. Hoff Tomáš Brůna Mark Borodovsky Mario Stanke TSEBRA: transcript selector for BRAKER
description	Abstract Background BRAKER is a suite of automatic pipelines, BRAKER1 and BRAKER2, for the accurate annotation of protein-coding genes in eukaryotic genomes. Each pipeline trains statistical models of protein-coding genes based on provided evidence and, then predicts protein-coding genes in genomic sequences using both the extrinsic evidence and statistical models. For training and prediction, BRAKER1 and BRAKER2 incorporate complementary extrinsic evidence: BRAKER1 uses only RNA-seq data while BRAKER2 uses only a database of cross-species proteins. The BRAKER suite has so far not been able to reliably exceed the accuracy of BRAKER1 and BRAKER2 when incorporating both types of evidence simultaneously. Currently, for a novel genome project where both RNA-seq and protein data are available, the best option is to run both pipelines independently, and to pick one, likely better output. Therefore, one or another type of the extrinsic evidence would remain unexploited. Results We present TSEBRA, a software that selects gene predictions (transcripts) from the sets generated by BRAKER1 and BRAKER2. TSEBRA uses a set of rules to compare scores of overlapping transcripts based on their support by RNA-seq and homologous protein evidence. We show in computational experiments on genomes of 11 species that TSEBRA achieves higher accuracy than either BRAKER1 or BRAKER2 running alone and that TSEBRA compares favorably with the combiner tool EVidenceModeler. Conclusion TSEBRA is an easy-to-use and fast software tool. It can be used in concert with the BRAKER pipeline to generate a gene prediction set supported by both RNA-seq and homologous protein evidence.
format	article
author	Lars Gabriel Katharina J. Hoff Tomáš Brůna Mark Borodovsky Mario Stanke
author_facet	Lars Gabriel Katharina J. Hoff Tomáš Brůna Mark Borodovsky Mario Stanke
author_sort	Lars Gabriel
title	TSEBRA: transcript selector for BRAKER
title_short	TSEBRA: transcript selector for BRAKER
title_full	TSEBRA: transcript selector for BRAKER
title_fullStr	TSEBRA: transcript selector for BRAKER
title_full_unstemmed	TSEBRA: transcript selector for BRAKER
title_sort	tsebra: transcript selector for braker
publisher	BMC
publishDate	2021
url	https://doaj.org/article/c79f7efdc41e45889aec4d525a2a106e
work_keys_str_mv	AT larsgabriel tsebratranscriptselectorforbraker AT katharinajhoff tsebratranscriptselectorforbraker AT tomasbruna tsebratranscriptselectorforbraker AT markborodovsky tsebratranscriptselectorforbraker AT mariostanke tsebratranscriptselectorforbraker
_version_	1718408166998278144

TSEBRA: transcript selector for BRAKER

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