Annotation and visualization of parasite, fungi and arthropod genomes with Companion.

Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.

Molecular Sequence Annotation* ; Arthropods*/genetics ; Software* ; Genome, Fungal*; Animals ; Genomics/methods ; Fungi/genetics ; Fungi/classification ; Genome/genetics ; Databases, Genetic ; Parasites/genetics ; Internet ; Humans

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.
(© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

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United Kingdom WT_ Wellcome Trust; ExposUM Institute of the University of Montpellier; 104111/Z/14/Z United Kingdom WT_ Wellcome Trust; University of Glasgow

Date Created: 20240516 Date Completed: 20240704 Latest Revision: 20240706

20240706

PMC11223846

10.1093/nar/gkae378

38752499