A beginner's guide to eukaryotic genome annotation

By Mark Yandell, Daniel Ence. Nature reviews genetics, 2012

617 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/3882fffb66f35eca632a5e2fe1c8a06477161076

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In Molecular Biology

Citations in the corpus

RepeatModeler2: automated genomic discovery of transposable element families (2019, methodology): “Notably they are used to annotate or “mask” the genome using RepeatMasker, which is a prerequisite for gene annotation (Yandell and Ence 2012).”
A simple method to control over-alignment in the MAFFT multiple sequence alignment program (2016, background): “Moreover, at the amino acid sequence level, a number of errors can be introduced due to difficulty in gene prediction (Brent, 2005; Gotoh et al. , 2014; Nagy and Patthy, 2013; Yandell and Ence, 2012).”
Genome Annotation and Curation Using MAKER and MAKER-P (2014, background): “See (Yandell and Ence, 2012) for a further discussion of AED.”
MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations1[W][OPEN] (2013, methodology): “In such cases, ab initio gene ﬁ nders perform poorly, requiring an evidence-driven means of genome annotation (Yandell and Ence, 2012).”
Next-Generation Sequencing — An Overview of the History, Tools, and “Omic” Applications (2016, methodology): “In an overview of the available tools and best practices for eukaryotic genome annotation, Yandell and Ence [103] pointed to five basic categories of annotation software: (1) Next-Generation Sequencing — An Overview of the History, Tools, and “Omic” Applications http://dx.”
A framework for incorporating evolutionary genomics into biodiversity conservation and management (2015, background): “At a minimum, annotation involves predicting the location and structure of a gene [117,118]; functional annotation then involves predicting the function of an identified gene, generally by comparison to related annotated genomes [119].”
Applications of next-generation sequencing to the study of biological invasions (2015, background): “Assembly quality can be assessed using different statistics, which offer a measure of genome completeness and contiguity (Miller et al., 2010; Yandell and Ence, 2012; Li et al., 2015).”
RepeatModeler2 for automated genomic discovery of transposable element families (2020, methodology): “Notably, they are used to annotate or “ mask ” the genome using RepeatMasker, which is a prerequisite for gene annotation (9).”
Future challenges in cephalopod research* (2014, background): “Part of the annotation process for a novel genome typically involves de novo gene prediction, a task that is known to be difficult and errorprone (Albertin et al., 2012; Yandell & Ence, 2012).”
The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics (2015, methodology): “After metagenome assembly, gene prediction and annotation are similar to the framework followed in whole genome characterization (Yandell and Ence, 2012; Richardson and Watson, 2013).”
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species (2013, background): “It has been noted that an assembly with a ‘gene-sized’ scaffold N50 length may be a good target for annotation [37].”