Tools & DBs
DNA, RNA & Genomes
The tools and databases developed at the I2BC are categorised by subject. The following are tools & databases to do with genomics data.
A workflow to build 3D models of genomes from raw HiC data and visually explore them
Identify Rho–independent transcription terminators in your sequences
Dynamically explore over 54000 replicons from 25000+ prokaryotic genomes
CRISPR database and tools to detect and view CRISPRs and cas genes in sequences
Dynamically explore a pre-calculated database of de novo emerged genes detected using phylostratigraphy and synteny, and run your own predictions using the DENSE pipeline
A computational pipeline for DETection of non-conding Rna in PROKaryotes
Easy RNA Profile IdentificatioN software, an RNA motif search programme
Predict specific protein DNA binding sites in prokaryotic genomes
Explore conservation and evolution of fungal metabolisms in 165 different species
HiCstuff
A webservice that runs the first steps of Hi-C analysis from fastq files and reference genomes.
Collaborative database to facilitate microbe genotyping (including pathogenic bacteria) essentially for epidemiological purposes.
View and explore identified ncRNA clusters in 1000+ sequenced bacterial genomes
ORENZA
An up-to-date database of orphan enzyme activities i.e. reported activities without known sequences within the major protein databases
A Database for Paramecium species to provide resources for functional and comparative genomics to the community
PARamecium Toolbox for Interspersed DNA Elimination Studies
Explore the complete genome and microarray data for strain S mat+ P. anserina
Display experimental data of a whole-genome mapping of 5′ RNA ends in Enterococcus faecalis
Interactively explore a database of 765 protein-RNA interfaces and their evolutionary relationships
Detect and analyse synteny breaks between (small) genomes
View and explore the synteny of protein sequences between +49 000 prokaryotic genomes
A webserver to analyse and manipulate DNA & RNA sequences
Source code: https://github.com/Transipedia/
Transcription Units by Coverage
Search your protein/DNA sequences against a complete database of natural plasmids and explore their matching plasmid synteny maps.