Other databases relevant to toxin-antitoxin systems:
  • : A bacterial Toxin-Antitoxin Systems database
  • : database of bacterial type II toxin-antitoxin loci
  • : Rapid Automated Scan for Toxins and Antitoxins in Bacteria (no longer maintained)
  • : comprehensive database of protein structural data on toxin-antitoxin systems (no longer maintained)

T1TAdb was built using the following software and tools:
  • Structure analysis
    • RNAMotif: identification of segments in genome sequences that can adopt a predefined 2D structure
    • RNASurface: identification of structured segments in genome sequences
    • IntaRNA: prediction of RNA-RNA interactions
    • ViennaRNA: prediction and comparison of RNA 2D structures
    • mfold: 2D structure prediction of nucleic acids
    • MAFFT: multiple sequence alignment (with or without incorporation of structural information)
    • VARNA: drawing of RNA 2D structure diagrams
    • R2R: drawing of RNA 2D structure diagrams
    • R-chie: plotting arc diagrams of RNA 2D structures along with sequence alignments
    • PSIPRED: 2D structure prediction of proteins
    • POLYVIEW-2D: drawing of protein 2D structure diagrams
    • ProtScale: hydrophobicity plot of proteins

  • Sequence analysis
    • BLAST: sequence similarity search
    • EMBOSS: software for molecular sequence data analysis
    • bedtools: toolset for genome analysis and arithmetic
    • InterProScan: automatic annotation of protein sequences based on signatures
    • FASTX-Toolkit: tools for Short-Reads FASTA/FASTQ files preprocessing

  • Visualization tools
    • CGView: drawing of genomic maps
    • IGV.js: JavaScript version of the Integrated Genome Viewer
    • Gviz: visualization of genomic data in R
    • JSAV: sequence alignment viewer in JavaScript
    • FlaGs2: comparison of gene neighborhoods
    • BioJS: library of visualization tools for biological data analysis in JavaScript

  • Development tools
    • CentOS: CentOS Linux operating system
    • Apache: HTTP webserver
    • PostgreSQL: relational SQL database system
    • PERL: PERL programming language
    • Catalyst: framework for website development in PERL
    • PERL Template Toolkit: webpage design in PERL
    • BioPerl: library of modules for biological data analysis in PERL
    • R: software environment for statistical computing and graphics
    • W3schools: tutorials and libraries for web programming in HTML, CSS, and JavaScript
    • CSS Script: JavaScript and CSS libraries for web design
    • WebsiteSetup: tutorials for website setup, developpment, and programming
    • Google Analytics: tools to analyze website usage statistics