ArticleBMC bioinformatics2009
Quantitative measures for the management and comparison of annotated genomes.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
85 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Effect of Methodological Considerations on the Construction of Gene-Based Plant Pan-genomes.Genome biology and evolution · 2023Pooled it
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- Reconstruction and analyses of genome-scaleMetabolic engineering communications · 2024Article
- Comparative genomics of Plasmodium yoelii nigeriensis N67 and N67C: genome-wide polymorphisms, differential gene expression, and drug resistance.BMC genomics · 2024Article
- Bank vole genomics links determinate and indeterminate growth of teeth.BMC genomics · 2024Article
- First draft reference genome and annotation of the alternative oil species Physaria fendleri.G3 (Bethesda, Md.) · 2024Article
- Genome report: First reference genome of Vaccinium floribundum Kunth, an emblematic Andean species.G3 (Bethesda, Md.) · 2024Article
- Genomics of ecological adaptation in Canary IslandEcology and evolution · 2024Article
- Complete genome of the Medicago anthracnose fungus,Microbial genomics · 2024Article
- Vole genomics links determinate and indeterminate growth of teeth.bioRxiv : the preprint server for biology · 2024Article
- Two telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis.Nature communications · 2024Article
- De Novo Genome Assembly for the Coppery Titi Monkey (Plecturocebus cupreus): An Emerging Nonhuman Primate Model for Behavioral Research.Genome biology and evolution · 2024Article
- First whole-genome sequence and assembly of the Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), a critically endangered species, using Oxford Nanopore Technologies.G3 (Bethesda, Md.) · 2024Article
- Brassicaceae display variation in efficiency of photorespiratory carbon-recapturing mechanisms.Journal of experimental botany · 2023Article
- Environmental gradients reveal stress hubs pre-dating plant terrestrialization.Nature plants · 2023Article
- Expanding the genetic toolbox of Rhodotorula toruloides by identification and validation of six novel promoters induced or repressed under nitrogen starvation.Microbial cell factories · 2023Article
- Chromosome-level genome assembly of the Asian aspen Populus davidiana Dode.Scientific data · 2023Article
- Decontamination and Annotation of the Draft Genome Sequence of the Oomycete Lagenidium giganteum ARSEF 373.Microbiology resource announcements · 2023Article
25 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
backgroundThe ever-increasing number of sequenced and annotated genomes has made management of their annotations a significant undertaking, especially for large eukaryotic genomes containing many thousands of genes. Typically, changes in gene and transcript numbers are used to summarize changes from release to release, but these measures say nothing about changes to individual annotations, nor do they provide any means to identify annotations in need of manual review.
resultsIn response, we have developed a suite of quantitative measures to better characterize changes to a genome's annotations between releases, and to prioritize problematic annotations for manual review. We have applied these measures to the annotations of five eukaryotic genomes over multiple releases -- H. sapiens, M. musculus, D. melanogaster, A. gambiae, and C. elegans.
conclusionOur results provide the first detailed, historical overview of how these genomes' annotations have changed over the years, and demonstrate the usefulness of these measures for genome annotation management.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.