ArticleNucleic acids research2024
Annotation and visualization of parasite, fungi and arthropod genomes with Companion.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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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
13 citing papers in PubMed.
- De Novo Assembly of the Trypanosoma congolense Genome Reveals an Organization Influenced by Antigenic Variation but Distinct from Trypanosoma brucei.Genome biology and evolution · 2026Article
- Draft genome sequence of the peptaibol producerMicrobiology resource announcements · 2026Article
- Single-cell sequencing reveals unexpected genetic diversity amongMicrobial genomics · 2026Article
- Circulation of fluconazole-resistant Candida auris in Peru confirmed by genomic analysis.Memorias do Instituto Oswaldo Cruz · 2026Article
- upsML: A high-accuracy machine learning classifier for predicting Plasmodium falciparum var gene upstream groups.PloS one · 2026Article
- Intra-strain genetic heterogeneity in Toxoplasma gondii ME49: Oxford Nanopore long-read sequencing reveals copy number variation in the ROP8-ROP2A locus.BMC genomics · 2025Article
- Leishmania mexicana telomeres at high resolution: Ku80, TERT, and alternative lengthening mechanisms.BMC genomics · 2025Article
- Improved assembly of theMicrobiology resource announcements · 2025Article
- Microbial succession and interaction in vacuum-packed beef: a longitudinal study of bacterial and fungal dynamics.NPJ science of food · 2025Article
- Genome drafts ofMicrobiology resource announcements · 2025Article
- The genome sequence of the Gypsy Moth,Wellcome open research · 2025Article
- Genomic evolution of enteric pathogens: mechanisms of pathogenicity and diagnostic innovations.Frontiers in microbiology · 2025Review
- Assembled genome of an EthiopianMicrobiology resource announcements · 2024Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
As sequencing genomes has become increasingly popular, the need for annotation of the resulting assemblies is growing. Structural and functional annotation is still challenging as it includes finding the correct gene sequences, annotating other elements such as RNA and being able to submit those data to databases to share it with the community. Compared to de novo assembly where contiguous chromosomes are a sign of high quality, it is difficult to visualize and assess the quality of annotation. We developed the Companion web server to allow non-experts to annotate their genome using a reference-based method, enabling them to assess the output before submitting to public databases. In this update paper, we describe how we have included novel methods for gene finding and made the Companion server more efficient for annotation of genomes of up to 1 Gb in size. The reference set was increased to include genomes of interest for human and animal health from the fungi and arthropod kingdoms. We show that Companion outperforms existing comparable tools where closely related references are available.
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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.