Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
By Brian J. Haas, Steven L. Salzberg, Wei Zhu, Mihaela Pertea, Jonathan E. Allen, Joshua Orvis, Owen White, C. R. Buell, Jennifer R. Wortman. Genome Biology, 2007
3,430 citations recorded by the source corpus.
EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/8262175d3d9fe59fe955a261a5ad1763db0e51e2
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Citations in the corpus
- Genome evolution across 1,011 Saccharomyces cerevisiae isolates (2018, positive): “We independently ran the three individual components (RATT 56 , YGAP 57 and MAKER 58 ) for gene annotation, and subsequently integrated their results using EVM 59 .”
- A complete Cannabis chromosome assembly and adaptive admixture for elevated cannabidiol (CBD) content (2018, methodology): “Repetitive sequence was identified using the set union of three programs: RepeatMasker, Tephra, and Red (44).”
- A beginner's guide to eukaryotic genome annotation (2012, background): “EVM allows the user to set expected evidence error rates manually or to learn them from a training set.”
- GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins (2020, neutral): “Therefore, ab initio gene finders [e.g. GENSCAN (13), Gen-eMark.hmm (14), AUGUSTUS (15) or GeneID (16)] have been a necessary part of genome annotation tools and pipelines [e.g. GNOMON (17), PASA (18) and Ensembl (19)].”
- TSEBRA: transcript selector for BRAKER (2021, methodology): “A prominent combiner tool is the openly accessible 43 EVidenceModeler (EVM) [28].”