ArticlePloS one2013
ORFcor: identifying and accommodating ORF prediction inconsistencies for phylogenetic analysis.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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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
11 citing papers in PubMed.
- Article
- Plant-PathogenicmBio · 2023Article
- A Large-Scale Genome-Based Survey of Acidophilic Bacteria Suggests That Genome Streamlining Is an Adaption for Life at Low pH.Frontiers in microbiology · 2022Article
- AssessORF: combining evolutionary conservation and proteomics to assess prokaryotic gene predictions.Bioinformatics (Oxford, England) · 2020Article
- Upregulation and Identification of Antibiotic Activity of a Marine-Derived Streptomyces sp. via Co-Cultures with Human Pathogens.Marine drugs · 2017Article
- Draft Genome Sequence of Streptomyces sp. Strain PTY087I2, Isolated from Styela canopus, a Panamanian Tunicate.Genome announcements · 2016Article
- Prediction of Toxin Genes from Chinese Yellow Catfish Based on Transcriptomic and Proteomic Sequencing.International journal of molecular sciences · 2016Article
- Article
- A Novel Quality Measure and Correction Procedure for the Annotation of Microbial Translation Initiation Sites.PloS one · 2015Article
- Estimating overannotation across prokaryotic genomes using BLAST+, UBLAST, LAST and BLAT.BMC research notes · 2014Article
- eCAMBer: efficient support for large-scale comparative analysis of multiple bacterial strains.BMC bioinformatics · 2014Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
The high-throughput annotation of open reading frames (ORFs) required by modern genome sequencing projects necessitates computational protocols that sometimes annotate orthologous ORFs inconsistently. Such inconsistencies hinder comparative analyses by non-uniformly extending or truncating 5' and/or 3' sequence ends, causing ORFs that are in fact identical to artificially diverge. Whereas strategies exist to correct such inconsistencies during whole-genome annotation, equivalent software designed to correct subsets of these data without genome reannotation is lacking. We therefore developed ORFcor, which corrects annotation inconsistencies using consensus start and stop positions derived from sets of closely related orthologs. ORFcor corrects inconsistent ORF annotations in diverse test datasets with specificities and sensitivities approaching 100% when sufficiently related orthologs (e.g., from the same taxonomic family) are available for comparison. The ORFcor package is implemented in Perl, multithreaded to handle large datasets, includes related scripts to facilitate high-throughput phylogenomic analyses, and is freely available at www.currielab.wisc.edu/downloads.html.
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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.