Predicting Genes in Single Genomes with AUGUSTUS
By Katharina Jasmin Hoff, Mario Stanke. Current Protocols in Bioinformatics, 2018
355 citations recorded by the source corpus.
AUGUSTUS is a tool for finding protein‐coding genes and their exon‐intron structure in genomic sequences. It does not necessarily require additional experimental input, as it can be applied in so‐called ab initio mode. However, extrinsic evidence from various sources such as transcriptome sequencing or the annotations of closely related genomes can be integrated in order to improve the accuracy and completeness of the annotation. AUGUSTUS can be applied to single genomes, or simultaneously to several aligned genomes. Here, we describe steps required for training AUGUSTUS for the annotation of individual genomes and the steps to do the actual structural annotation. Further, we describe the generation and integration of evidence from various sources of extrinsic evidence. © 2018 by John Wiley & Sons, Inc.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/9a71dfa19476a9639d3b88e99b3c44c7573c5017
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In Molecular Biology
- Mark Borodovsky
- Alexandre Lomsadze
- Tomás Bruna
- Katharina Jasmin Hoff
- Mario Stanke
- Paschalia Kapli
- Ziheng Yang
- Maximilian J. Telford
Citations in the corpus
- Phylogenetic tree building in the genomic age (2020, positive): “Initial gene sequence data can be derived either from gene predictions based on genome sequences (even from draft-quality genomes) or from transcriptomes generated by sequencing libraries derived from mRNA 12 (Fig.”
- GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins (2020, neutral): “AUGUSTUS (1), GeneMark-ET (2), EuGene (3,4) and mGene.”
- BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database (2020, background): “Such simpler organized genes are therefore down-sampled as described earlier [6].”