TransPrise: a novel machine learning approach for eukaryotic promoter prediction
- Published
- Accepted
- Subject Areas
- Computational Biology, Genomics, Data Mining and Machine Learning
- Keywords
- promoter, transcription start site, machine learning
- Copyright
- © 2019 Pachganov et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2019. TransPrise: a novel machine learning approach for eukaryotic promoter prediction. PeerJ Preprints 7:e27844v1 https://doi.org/10.7287/peerj.preprints.27844v1
Abstract
As interest in genetic resequencing increases, so does the need for effective mathematical, computational, and statistical approaches. One of the difficult problems in genome annotation is determination of precise positions of transcription start sites. In this paper we present TransPrise - an efficient deep learning tool for prediction of positions of eukaryotic transcription start sites. TransPrise offers significant improvement over existing promoter-prediction methods. To illustrate this, we compared predictions of TransPrise with the TSSPlant approach for well annotated genome of Oryza sativa. Using a computer equipped with a graphics processing unit, the run time of TransPrise is 250 minutes on a genome of 374 Mb long. We provide the full basis for the comparison and encourage users to freely access a set of our computational tools to facilitate and streamline their own analyses. The ready-to-use Docker image with all necessary packages, models, code as well as the source code of the TransPrise algorithm are available at ( http://compubioverne.group /). The source code is ready to use and customizable to predict TSS in any eukaryotic organism.
Author Comment
This is a submission to PeerJ for review.