FiltDeTox classification of toxin candidates in the paired-end transcriptome of the deep-sea zoanthid Zibrowius primnoidus
Description
This dataset contains the outputs of FiltDeTox, a rule-based post-processing framework built on top of DeTox, applied to the paired-end transcriptome of the deep-sea zoanthid Zibrowius primnoidus. Starting from DeTox results, FiltDeTox combines DeTox flags (Rating), secretion predictions (WoLFPSort), HMMER-based mapping to VenomZone toxin families, Pfam toxin domains and toxin-related keywords to classify each ORF into four categories: Toxins-Candidates, Unlikely-Toxins, SCRs-WA (secreted cysteine-rich sequences with weak/absent annotation) and Non-Toxins. The dataset provides: • Full_Classified_Data.tsv: complete table with all DeTox ORFs, annotations and the FiltDeTox_Classification column. • Four per-class tables (Toxins_Candidates.tsv, Unlikely_Toxins.tsv, SCRs_WA.tsv, Non_Toxins.tsv) plus FiltDeTox_Stats.tsv summarising ORF counts per class. • Per-class mature and precursor FASTA files (…_mature.fasta and …_precursor.fasta) for all four categories. • Per-class “full-length” TSVs (…_full-length.tsv), precursor FASTA files restricted to complete sequences (…_precursor_full-length-seqs.fasta) and small stats files (…_full-length_stats.txt). • Pfam_Domain_Summary_with_ORFs_Genes.tsv: domain-wise summary for Toxins-Candidates, including numbers of ORFs/transcripts/genes, total TPM and associated IDs. • Plot files (PNG and PDF): stacked barplots for FiltDeTox classes and DeTox flags, nested pie charts combining classes and flags, a pie chart of flags within Toxins-Candidates, and a combined dendrogram + dot plot of Pfam domains and their ORF/TPM profiles. • These files provide a classified and sequence-resolved view of the DeTox-derived toxin landscape in Zibrowius primnoidus, ready for downstream comparative and functional analyses. RNA-seq data are available under BioProject PRJNA1223694.
Files
Steps to reproduce
The files deposited in this dataset were obtained by: Running DeTox v1.1.3 on the paired-end transcriptome of Zibrowius primnoidus, following the pipeline at https://github.com/Hyperdiverseproject/DeTox and the description in Allan Ringeval et al., “DeTox: a pipeline for the detection of toxins in venomous organisms”, Briefings in Bioinformatics, Volume 25, Issue 2, March 2024, bbae094, https://doi.org/10.1093/bib/bbae094. • Merging DeTox outputs with ToxinKeyMatch results and HMMER-based mapping to VenomZone toxin families. • Applying the FiltDeTox R workflow (ToxRecov.R) to assign FiltDeTox classes, generate per-class tables and sequence FASTAs, compute domain-level summaries and produce the figures and full-length subsets included here.
Institutions
- Stazione Zoologica Anton Dohrn
Categories
Funders
- This work was supported by Centro Ricerche ed Infrastrutture Marine Avanzate in Calabria (CRIMAC) - Fondo FSC 2014-2020 - Piano Stralcio «Ricerca e Innovazione 2015-2017» – Programma Nazionale Infrastrutture di Ricerca (PNIR), CUP C64I20000320001.