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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

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

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Author(s):
Nachtigall, Pedro G. [1] ; Rautsaw, Rhett M. [2] ; Ellsworth, Schyler A. [3] ; Mason, Andrew J. [4] ; Rokyta, Darin R. [5] ; Parkinson, Christopher L. [6] ; Junqueira-de-Azevedo, Inacio L. M. [7]
Total Authors: 7
Affiliation:
[1] Inst Butantan, Sao Paulo - Brazil
[2] Clemson Univ, Biol Sci, Clemson, SC 29631 - USA
[3] Florida State Univ, Ecol & Evolut, Tallahassee, FL 32306 - USA
[4] Ohio State Univ, Columbus, OH 43210 - USA
[5] Florida State Univ, Tallahassee, FL 32306 - USA
[6] Clemson Univ, Clemson, SC 29631 - USA
[7] Inst Butantan, Appl Toxinol Lab, Sao Paulo - Brazil
Total Affiliations: 7
Document type: Journal article
Source: BRIEFINGS IN BIOINFORMATICS; v. 22, n. 5 SEP 2021.
Web of Science Citations: 0
Abstract

Motivation: 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. Supplementary Data: Supplementary data are available online at https://academic.oup.com/bib. (AU)

FAPESP's process: 16/50127-5 - Dimensions US-BIOTA São Paulo: scales of biodiversity: integrated studies of snake venom evolution and function across multiple levels of diversity
Grantee:Inácio de Loiola Meirelles Junqueira de Azevedo
Support type: BIOTA-FAPESP Program - Thematic Grants
FAPESP's process: 18/26520-4 - Characterization of the interrelationship between transcriptomes, miRNomes and proteomes from the venom glands of Bothrops fonsecai and Bothrops cotiara
Grantee:Pedro Gabriel Nachtigall
Support type: Scholarships in Brazil - Post-Doctorate