ToxCodAn: a new toxin annotator and guide to venom gland transcriptomics

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dc.contributorLETA - Laboratório de Toxinologia Aplicadapt_BR
dc.contributorCentro de Toxinas, Resposta-imune e Sinalização Celular (CeTICS)pt_BR
dc.contributor.authorNachtigall, Pedro Gabrielpt_BR
dc.contributor.authorRautsaw, Rhett Mpt_BR
dc.contributor.authorEllsworth, Schyler Apt_BR
dc.contributor.authorMason, Andrew Jpt_BR
dc.contributor.authorRokyta, Darin Rpt_BR
dc.contributor.authorParkinson, Christopher Lpt_BR
dc.contributor.authorJunqueira-de-Azevedo, Inácio de Loiola Meirellespt_BR
dc.identifier.citationNachtigall PG, Rautsaw RM, Ellsworth SA, Mason AJ, Rokyta DR, Parkinson CL, et al. ToxCodAn: a new toxin annotator and guide to venom gland transcriptomics. Brief Bioinform. 2021 Apr;in press. doi:10.1093/bib/bbab095.pt_BR
dc.description.abstractMotivation: Next-generation sequencing has become exceedingly common and has transformed our ability to explore nonmodel systems. In particular, transcriptomics has facilitated the study of venom and evolution of toxins in venomous lineages; however, many challenges remain. Primarily, annotation of toxins in the transcriptome is a laborious and time-consuming task. Current annotation software often fails to predict the correct coding sequence and overestimates the number of toxins present in the transcriptome. Here, we present ToxCodAn, a python script designed to perform precise annotation of snake venom gland transcriptomes. We test ToxCodAn with a set of previously curated transcriptomes and compare the results to other annotators. In addition, we provide a guide for venom gland transcriptomics to facilitate future research and use Bothrops alternatus as a case study for ToxCodAn and our guide. Results: Our analysis reveals that ToxCodAn provides precise annotation of toxins present in the transcriptome of venom glands of snakes. Comparison with other annotators demonstrates that ToxCodAn has better performance with regard to run time (⁠>20x faster), coding sequence prediction (⁠>3x more accurate) and the number of toxins predicted (generating >4x less false positives). In this sense, ToxCodAn is a valuable resource for toxin annotation. The ToxCodAn framework can be expanded in the future to work with other venomous lineages and detect novel toxins.pt_BR
dc.description.sponsorshipFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)pt_BR
dc.description.sponsorshipNational Science Foundation (NSF)pt_BR
dc.relation.ispartofBriefings in Bioinformaticspt_BR
dc.rightsOpen Accesspt_BR
dc.titleToxCodAn: a new toxin annotator and guide to venom gland transcriptomicspt_BR
dc.contributor.externalClemson Universitypt_BR
dc.contributor.externalFlorida State Universitypt_BR
dc.contributor.externalOhio State Universitypt_BR
dc.relation.ispartofabbreviatedBrief Bioinformpt_BR
dc.identifier.citationabntin press, abr. 2021pt_BR
dc.identifier.citationvancouver2021 Apr;in presspt_BR
dc.contributor.butantanNachtigall, Pedro Gabriel|:Aluno|:Laboratório Especial de Toxinologia Aplicada (LETA):Centro de Toxinas, Resposta-imune e Sinalização Celular (CeTICS)|:PrimeiroAutor:Autor de correspondênciapt_BR
dc.contributor.butantanJunqueira-de-Azevedo, Inácio de Loiola Meirelles|:Pesquisador|:Laboratório Especial de Toxinologia Aplicada (LETA):Centro de Toxinas, Resposta-imune e Sinalização Celular (CeTICS)pt_BR
dc.sponsorship.butantanFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)¦¦ 2016/50127-5pt_BR
dc.sponsorship.butantanFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)¦¦2018/26520-4pt_BR
dc.sponsorship.butantanNational Science Foundation¦¦1145987pt_BR
dc.sponsorship.butantanNational Science Foundation¦¦1638902pt_BR
dc.sponsorship.butantanNational Science Foundation¦¦1822417pt_BR
dc.sponsorship.butantanNational Science Foundation¦¦1638879pt_BR
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