Genome Annotation and Curation Using MAKER and MAKER-P
By Michael Campbell, Carson Holt, Barry Moore, Mark Yandell. Current Protocols in Bioinformatics, 2014
652 citations recorded by the source corpus.
This unit describes how to use the genome annotation and curation tools MAKER and MAKER‐P to annotate protein‐coding and noncoding RNA genes in newly assembled genomes, update/combine legacy annotations in light of new evidence, add quality metrics to annotations from other pipelines, and map existing annotations to a new assembly. MAKER and MAKER‐P can rapidly annotate genomes of any size, and scale to match available computational resources. © 2014 by John Wiley & Sons, Inc.
Subfields: Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/eccd5e7cba65b72216c89224c9daa24fc5398670
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Citations in the corpus
- JBrowse: a dynamic web platform for genome visualization and analysis (2016, methodology): “A few examples of tools that use JBrowse include the web version of Apollo [12], SeqWare [13], DNA subway [14], GenSAS [15], Maker [16, 17], and Afra [18].”
- BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics (2017, methodology): “MAKER (Campbell et al. 2014) can employ the outputs of preliminary annotation runs to automatically retrain and improve its gene prediction algorithm.”
- JCVI: A versatile toolkit for comparative genomics analysis (2024, methodology): “The driver scripts are able to control the life cycle of an annotation project, including the training of ab initio gene predictors, postprocessing of structural annotations (e.g., MAKER [25]), and functional annotations (e.g., AHRD [26]).”
- BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database (2020, neutral): “…metrics are less precise in assessment of accuracy of gene prediction than the methods comparing coordinates of predicted and annotated genes and computing Sn, Sp and F1 values. such as ab initio gene predictions, mapped RNA-seq reads as well as alignments of proteins to the genome (33,40,41).”