ArticleNucleic acids research2016
Companion: a web server for annotation and analysis of parasite genomes.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 93 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
93 citing papers in PubMed, 141 citations in OpenAlex.
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- Characterization of ovine abortion in Uruguay reveals extensive non-clonal diversity and multiple evolutionary origins of Toxoplasma gondii.Scientific reports · 2026Article
- Nuclear Genome Assembly and Annotation of Kinetoplastids.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Novel zoonotic cases of Plasmodium simium from São Paulo with a reference genome of the Brazilian strain.Scientific reports · 2025Article
- Insights on genomic profiles of drug resistance and virulence in a cohort of Leishmania infantum isolates from the Mediterranean area.Parasites & vectors · 2025Article
- Exploring homology detection via k-means clustering of proteins embedded with a large language model.Bioinformatics (Oxford, England) · 2025Article
- Genetic diversity and comparative genomics across Leishmania (Viannia) species.Communications biology · 2025Article
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- Genome assembly ofMicrobiology resource announcements · 2025Article
- Supersaturation mutagenesis reveals adaptive rewiring of essential genes among malaria parasites.Science (New York, N.Y.) · 2025Article
- Nanopore sequencing reveals that DNA replication compartmentalisation dictates genome stability and instability in Trypanosoma brucei.Nature communications · 2025Article
- Somy evolution in the honey bee infecting trypanosomatid parasite Lotmaria passim.G3 (Bethesda, Md.) · 2025Article
- Inter-chromosomal transcription hubs shape the 3D genome architecture of African trypanosomes.Nature communications · 2024Article
- Genome alteration of Leishmania orientalis under Amphotericin B inhibiting conditions.PLoS neglected tropical diseases · 2024Article
- Article
- Annotation and visualization of parasite, fungi and arthropod genomes with Companion.Nucleic acids research · 2024Article
- Comparative Genomics of the First ResistantJournal of fungi (Basel, Switzerland) · 2024Article
- Competitive fungal commensalism mitigates candidiasis pathology.The Journal of experimental medicine · 2024Article
- Draft genome ofMicrobiology resource announcements · 2024Article
33 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
7 authors at 3 institutions in 2 countries.
Funding
Abstract
Currently available sequencing technologies enable quick and economical sequencing of many new eukaryotic parasite (apicomplexan or kinetoplastid) species or strains. Compared to SNP calling approaches, de novo assembly of these genomes enables researchers to additionally determine insertion, deletion and recombination events as well as to detect complex sequence diversity, such as that seen in variable multigene families. However, there currently are no automated eukaryotic annotation pipelines offering the required range of results to facilitate such analyses. A suitable pipeline needs to perform evidence-supported gene finding as well as functional annotation and pseudogene detection up to the generation of output ready to be submitted to a public database. Moreover, no current tool includes quick yet informative comparative analyses and a first pass visualization of both annotation and analysis results. To overcome those needs we have developed the Companion web server (http://companion.sanger.ac.uk) providing parasite genome annotation as a service using a reference-based approach. We demonstrate the use and performance of Companion by annotating two Leishmania and Plasmodium genomes as typical parasite cases and evaluate the results compared to manually annotated references.
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What OpenQuestion holds
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.