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
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