Apollo: Democratizing genome annotation.
PLoS Computational Biology, 2019 Genome annotation is the process of identifying the location and function of a genome's encoded features. Improving the biological accuracy of annotation is a complex and iterative process requiring researchers to review and incorporate multiple sources ...
Nathan A Dunn +9 more
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Welcome to the big leaves: Best practices for improving genome annotation in non‐model plant genomes
Applications in Plant Sciences, 2023 Premise Robust standards to evaluate quality and completeness are lacking in eukaryotic structural genome annotation, as genome annotation software is developed using model organisms and typically lacks benchmarking to comprehensively evaluate the ...
Vidya S. Vuruputoor +10 more
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Galba: genome annotation with miniprot and AUGUSTUS. [PDF]
BMC Bioinformatics, 2023 The Earth Biogenome Project has rapidly increased the number of available eukaryotic genomes, but most released genomes continue to lack annotation of protein-coding genes. In addition, no transcriptome data is available for some genomes.
Brůna T +9 more
europepmc +3 more sources
RefSeq and the prokaryotic genome annotation pipeline in the age of metagenomes. [PDF]
Nucleic Acids Res, 2023 The Reference Sequence (RefSeq) project at the National Center for Biotechnology Information (NCBI) contains over 315 000 bacterial and archaeal genomes and 236 million proteins with up-to-date and consistent annotation.
Haft DH +10 more
europepmc +2 more sources
Manual curation for improved genome annotation of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni). [PDF]
PLoS ONEThe northern white rhinoceros (Ceratotherium simum cottoni) genome and annotation were previously published, but the annotation contained few genes, with many annotation misalignments, and nomenclature not matching HGNC/VGNC naming conventions, making ...
Elena Ruggeri +4 more
doaj +2 more sources
The rice genome annotation project: an updated database for mining the rice genome. [PDF]
Nucleic Acids ResRice (Oryza sativa L.) is a major cereal crop that provides calories across the world. With a small genome, rice has been used extensively as a model for genetic and genomic studies in the Poaceae.
Hamilton JP, Li C, Buell CR.
europepmc +2 more sources
Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing
Biology, 2020 Next-Generation Sequencing (NGS) has made it easier to obtain genome-wide sequence data and it has shifted the research focus into genome annotation. The challenging tasks involved in annotation rely on the currently available tools and techniques to ...
Girum Fitihamlak Ejigu, Jaehee Jung
doaj +2 more sources
BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA. [PDF]
Genome ResGene prediction has remained an active area of bioinformatics research for a long time. Still, gene prediction in large eukaryotic genomes presents a challenge that must be addressed by new algorithms.
Gabriel L +6 more
europepmc +2 more sources
BMC Bioinformatics, 2011 Background Second-generation sequencing technologies are precipitating major shifts with regards to what kinds of genomes are being sequenced and how they are annotated.
Holt Carson, Yandell Mark
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Capturing heart valve development with Gene Ontology
Frontiers in Genetics, 2023 Introduction: The normal development of all heart valves requires highly coordinated signaling pathways and downstream mediators. While genomic variants can be responsible for congenital valve disease, environmental factors can also play a role. Later in
Saadullah H. Ahmed +4 more
doaj +1 more source