TSEBRA: transcript selector for BRAKER

• Published in: BMC bioinformatics Vol. 22; no. 1; pp. 1 - 12
• Main Authors: Gabriel, Lars, Hoff, Katharina J., Brůna, Tomáš, Borodovsky, Mark, Stanke, Mario
• Format: Journal Article
• Language: English
• Published: London BioMed Central 25.11.2021; BioMed Central Ltd; Springer Nature B.V; BMC
• Subjects: Accuracy; Algorithms; Analysis; Annotations; Bioinformatics; Biomedical and Life Sciences; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Computer applications; Computer programs; Evidence integration; Gene prediction; Genes; Genetic code; Genetic transcription; Genome annotation; Genomes; Homology; Homology (Biology); Identification and classification; Life Sciences; Mathematical models; Methods; Microarrays; Pipelines; Predictions; Protein homology; Protein-coding genes; Proteins; Ribonucleic acid; RNA; RNA sequencing; RNA-seq; Software; Software development tools; Software engineering; Statistical analysis; Statistical models; Transcription; United States; Gene prediction; Protein-coding genes; Genome annotation; Protein homology; RNA-seq; Evidence integration
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-021-04482-0

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.