ArticleGigaScience2024
ToxCodAn-Genome: an automated pipeline for toxin-gene annotation in genome assembly of venomous lineages.
Article in GigaScience, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 14 citations in OpenAlex.
- From neuropeptides to toxins: illuminating the origins of venom complexity in cone snails.Molecular biology and evolution · 2026Article
- The Golden Lancehead Genome Reveals Distinct Selective Processes Acting on Venom Genes of an Island Endemic Snake.Genome biology and evolution · 2026Article
- Molecular mechanisms underlying early functional divergence in snake venom inferred from the genomes of two pitviper lineages.BMC biology · 2025Article
- From Neuropeptides to Toxins: Illuminating the Origins of Venom Complexity in Cone Snails.bioRxiv : the preprint server for biology · 2025Article
- Genome of the green-head ant, Rhytidoponera metallica, reveals mechanisms of toxin evolution in a genetically hyper-diverse eusocial species.Genome biology · 2025Article
- The gene regulatory mechanisms shaping the heterogeneity of venom production in the Cape coral snake.Genome biology · 2025Article
- A Segregating Structural Variant Defines Novel Venom Phenotypes in the Eastern Diamondback Rattlesnake.Molecular biology and evolution · 2025Article
- A Vision for VenomsBase: An Integrated Knowledgebase for the Study of Venoms and Their Applications.Integrative organismal biology (Oxford, England) · 2025Article
- VenomCap: An exon-capture probe set for the targeted sequencing of snake venom genes.Molecular ecology resources · 2024Article
- ToxCodAn-Genome: an automated pipeline for toxin-gene annotation in genome assembly of venomous lineages.GigaScience · 2024Article
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundThe rapid development of sequencing technologies resulted in a wide expansion of genomics studies using venomous lineages. This facilitated research focusing on understanding the evolution of adaptive traits and the search for novel compounds that can be applied in agriculture and medicine. However, the toxin annotation of genomes is a laborious and time-consuming task, and no consensus pipeline is currently available. No computational tool currently exists to address the challenges specific to toxin annotation and to ensure the reproducibility of the process.
resultsHere, we present ToxCodAn-Genome, the first software designed to perform automated toxin annotation in genomes of venomous lineages. This pipeline was designed to retrieve the full-length coding sequences of toxins and to allow the detection of novel truncated paralogs and pseudogenes. We tested ToxCodAn-Genome using 12 genomes of venomous lineages and achieved high performance on recovering their current toxin annotations. This tool can be easily customized to allow improvements in the final toxin annotation set and can be expanded to virtually any venomous lineage. ToxCodAn-Genome is fast, allowing it to run on any personal computer, but it can also be executed in multicore mode, taking advantage of large high-performance servers. In addition, we provide a guide to direct future research in the venomics field to ensure a confident toxin annotation in the genome being studied. As a case study, we sequenced and annotated the toxin repertoire of Bothrops alternatus, which may facilitate future evolutionary and biomedical studies using vipers as models.
conclusionsToxCodAn-Genome is suitable to perform toxin annotation in the genome of venomous species and may help to improve the reproducibility of further studies. ToxCodAn-Genome and the guide are freely available at https://github.com/pedronachtigall/ToxCodAn-Genome.
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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.