Tailored machine learning models for functional RNA detection in genome-wide screens

DOI10.5281/zenodo.8120827Zenodo8120827MaRDI QIDQ6708632FDOQ6708632

Dataset published at Zenodo repository.

Peter F. Stadler, Felix Kühnl, Jörg Fallmann, Christopher Klapproth, Siegfried Zöztsche, Sven Findeiß

Publication date: 6 July 2023

Copyright license: Creative Commons Attribution 4.0 International

Description

The prediction of noncoding RNA and protein coding genetic loci has received considerable attention in comparative genomics aiming in particular at the identification of properties of nucleotide sequences that are informative of their biological role in the cell. We present here a software framework for the alignment-based training, evaluation and application of machine learning models with user-defined parameters. Instead of focusing on the one-size-fits-all approach of pervasive \is annotation pipelines, we offer a framework for the structured generation and evaluation of models based on arbitrary features and input data, focusing on stable and explainable results. Furthermore, we showcase the usage of our software package in a full-genome screen of Drosophila melanogaster and evaluate our results against the well-known but much less flexible program RNAz.

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