BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts

(2015) Alison C Testa et al.   BMC GENOMICS

Current methods for automated annotation of protein-coding genes

(2015) KJ Hoff et al.   Current Opinion in Insect Science

SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models

(2014) Ian Reid et al.   BMC BIOINFORMATICS

Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm

(2014) Alexandre Lomsadze et al.   NUCLEIC ACIDS RESEARCH

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

(2008) V. Ter-Hovhannisyan et al.   GENOME RESEARCH