Evaluating Programs for Predicting Genes and Transcripts with RNA-Seq Support in Fungal Genomes.

Methods Mol Biol. 2018;1775:209-227

Authors: Reid I

Abstract

The steps needed to computationally predict genes and transcripts in fungal genomes with support from RNA-Seq data are described in detail for three prediction programs: CodingQuarry, BRAKER1, and Harfang. These programs predicted from 86% to 92% (Harfang) of the genes in a manually curated reference set for Aspergillus niger strain NRRL3. Genes with little or no RNA-Seq read coverage were predicted less successfully than genes with adequate coverage.

PMID: 29876820 [PubMed - indexed for MEDLINE]