Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi
By Jens Keilwagen, F. Hartung, Michael Paulini, Sven Twardziok, Jan Grau. BMC Bioinformatics, 2017
306 citations recorded by the source corpus.
Genome annotation is of key importance in many research questions. The identification of protein-coding genes is often based on transcriptome sequencing data, ab-initio or homology-based prediction. Recently, it was demonstrated that intron position conservation improves homology-based gene prediction, and that experimental data improves ab-initio gene prediction. Here, we present an extension of the gene prediction program GeMoMa that utilizes amino acid sequence conservation, intron position conservation and optionally RNA-seq data for homology-based gene prediction. We show on published benchmark data for plants, animals and fungi that GeMoMa performs better than the gene prediction programs BRAKER1, MAKER2, and CodingQuarry, and purely RNA-seq-based pipelines for transcript identification. In addition, we demonstrate that using multiple reference organisms may help to further improve the performance of GeMoMa. Finally, we apply GeMoMa to four nematode species and to the recently published barley reference genome indicating that current annotations of protein-coding genes may be refined using GeMoMa predictions. GeMoMa might be of great utility for annotating newly sequenced genomes but also for finding homologs of a specific gene or gene family. GeMoMa has been published under GNU GPL3 and is freely available at http://www.jstacs.de/index.php/GeMoMa.
Subfields: Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/c3400d3501e3b9d5cb63b550e6452b7a8211afe9
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Citations in the corpus
- TSEBRA: transcript selector for BRAKER (2021, methodology): “31 When heterogeneous extrinsic evidence sources are available, some genome annotation tools like 32 MAKER2 [20] and GeMoMa [21] integrate these different sources directly into the annotation 33 protocol.”
- BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database (2020, unknown): “This challenge is much smaller if a tool, like GeMoMa (49,50), is oriented on getting the protein information from closely related species.”