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GeneMark-EP and -EP+: automatic eukaryotic gene prediction supported by spliced aligned proteins

Tomas Bruna, Alexandre Lomsadze, Mark Borodovsky
doi: https://doi.org/10.1101/2019.12.31.891218
Tomas Bruna
1School of Biological Sciences, Georgia Institute of Technology, Atlanta GA 30332, USA
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Alexandre Lomsadze
2Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta GA 30332, USA
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Mark Borodovsky
1School of Biological Sciences, Georgia Institute of Technology, Atlanta GA 30332, USA
2Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta GA 30332, USA
3School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta GA 30332, USA
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  • For correspondence: borodovsky@gatech.edu
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Abstract

We have made several steps towards creating fast and accurate algorithm for gene prediction in eukaryotic genomes. First, we introduced an automated method for efficient ab initio gene finding, GeneMark-ES, with parameters trained in iterative unsupervised mode. Next, in GeneMark-ET we proposed a method of integration of unsupervised training with information on intron positions revealed by mapping short RNA reads. Now we describe GeneMark-EP, a tool that utilizes another source of external information, a protein database, readily available prior to a start of a sequencing project. The new algorithm and software tool integrate information produced by proteins spliced aligned to genomic regions into model training and gene prediction steps. A specialized pipeline, ProtHint, makes processing the results of mapping of multiple proteins to a genomic region where a protein from the same family is likely encoded. GeneMark-EP uses the hints from ProtHint to improve estimation of model parameters as well as to adjust co-ordinates of predicted genes if they disagree with the most reliable hints (the -EP+ mode). Tests conducted with GeneMark-EP and -EP+ have demonstrated that the gene prediction accuracy is higher than one of GeneMark-ES, particularly in large eukaryotic genomes.

Footnotes

  • ↵† Joint first authors

  • https://github.com/gatech-genemark/GeneMark-EP-plus

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted January 02, 2020.
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GeneMark-EP and -EP+: automatic eukaryotic gene prediction supported by spliced aligned proteins
Tomas Bruna, Alexandre Lomsadze, Mark Borodovsky
bioRxiv 2019.12.31.891218; doi: https://doi.org/10.1101/2019.12.31.891218
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GeneMark-EP and -EP+: automatic eukaryotic gene prediction supported by spliced aligned proteins
Tomas Bruna, Alexandre Lomsadze, Mark Borodovsky
bioRxiv 2019.12.31.891218; doi: https://doi.org/10.1101/2019.12.31.891218

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