Welcome to the big leaves: Best practices for improving genome annotation in non‐model plant genomes [PDF]
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
doaj +4 more sources
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
doaj +8 more sources
A quick guide for student-driven community genome annotation [PDF]
PLoS Comput. Biol., 2018 High quality gene models are necessary to expand the molecular and genetic tools available for a target organism, but these are available for only a handful of model organisms that have undergone extensive curation and experimental validation over the course of many years.
Benoit, Joshua B. +10 more
arxiv +6 more sources
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes [PDF]
Nucleic Acids Research, 2005 The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the Project to Annotate 1000 Genomes.
Ross Overbeek
semanticscholar +8 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
Genome annotation for clinical genomic diagnostics: strengths and weaknesses [PDF]
Genome Medicine, 2017 The Human Genome Project and advances in DNA sequencing technologies have revolutionized the identification of genetic disorders through the use of clinical exome sequencing.
Charles A. Steward +5 more
doaj +3 more sources
Evaluation of three automated genome annotations for Halorhabdus utahensis. [PDF]
PLoS ONE, 2009 Genome annotations are accumulating rapidly and depend heavily on automated annotation systems. Many genome centers offer annotation systems but no one has compared their output in a systematic way to determine accuracy and inherent errors. Errors in the
Peter Bakke +12 more
doaj +6 more sources
Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop [PDF]
Viruses, 2010 Improvements in DNA sequencing technologies portend a new era in virology and could possibly lead to a giant leap in our understanding of viral evolution and ecology.
Qiandong Zeng +14 more
doaj +5 more sources
Improved Reference Genome Annotation of Brassica rapa by Pacific Biosciences RNA Sequencing. [PDF]
Front Plant Sci, 2022 The species Brassica rapa includes several important vegetable crops. The draft reference genome of B. rapa ssp. pekinensis was completed in 2011, and it has since been updated twice. The pangenome with structural variations of 18 B.
Zhang Z +8 more
europepmc +2 more sources
Improved annotation of 3-prime untranslated regions and complex loci by combination of strand-specific Direct RNA Sequencing, RNA-seq and ESTs [PDF]
PLoS ONE 9(4) (2014): e94270, 2013 The reference annotations made for a genome sequence provide the framework for all subsequent analyses of the genome. Correct annotation is particularly important when interpreting the results of RNA-seq experiments where short sequence reads are mapped against the genome and assigned to genes according to the annotation. Inconsistencies in annotations
A Derti +52 more
arxiv +7 more sources