Service list

A web service for the structural annotation of protein-protein interaction networks. 

A database framework widely used to support model organism databases. 

InterPro classifies proteins into families and predicts the presence of important domains and sites.

iPath is a web-based tool for the visualization and analysis of cellular pathways. Based on current annotations (such as KEGG), it provides pathway maps for primary cellular metabolism as well as for some additional secondary metabolite synthesis and regulatory pathways. Users can map their own data onto these pathway maps. Due to its navigation and customization functions, iPATH thus allows users to easily explore and analyze the functional and metabolic capabilities of their (meta-)genomic data sets. Part of the Microbiome Analysis Toolbox. 

Integrated Proteogenomics DataBases an open source database that provides integrated annotations, predictions and a six-frame translation for one respective genome sequence in an easily usable format, both as a search DB (FASTA format) with informative identifiers and a GFF file that integrates all annotations and identifiers.

Non-coding genome sequences and genetic network tools. The IRESite presents experimental evidence of many eukaryotic viral and cellular internal ribosome entry site (IRES) regions.

A suite of open source tools and formats to enable standards-compliant collection, curation, management, publication and reuse of experiments. 

Models genome-wide expression data in terms of genome-wide annotations of regulatory sites. For a given expression data-set it infers the key transcription regulators, their sample- dependent activities, and their genome-wide targets. 

A means for determining the pattern occurring in groups of isogenic individual mutations (SNP, deletion, insertion)

The Italian COVID-19 Data Portal provides information, guidelines, tools and services to support researchers in creating and sharing research data on COVID-19.

Interactive Tree Of Life (iTOL) is an online tool for the display and manipulation of phylogenetic trees. It provides a large variety of tree layouts, drawing and annotation features including circular tree layout, which is well-suited particularly for mid-sized trees (up to several thousand leaves). Tree displays can be exported in several graphical formats, both bitmap and vector based. Part of the Microbiome Analysis Toolbox. 

ITSoneDB is a comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences.

A Galaxy-based workbench providing established tools (e.g BioMaS, Mothur and qiime2) targeted at global taxonomic analysis of eukaryotic communities based on Internal Transcribed Spacer 1 variants high-throughput sequencing.

A curated database of drug targets, prescription medicines and experimental drugs.

Tool for determining disordered protein regions

Jalview is a Win/Mac/Linux/Web interactive graphical interface and command line tool for molecular sequence, alignment and 3D structure bioinformatics resource interoperability.

JAMDA docks small molecules into protein binding sites.

An open access database of manually curated, non-redundant transcription factor (TF) binding profiles

KEGGanim is a tool for visualizing data in the context of biological pathways. KEGGanim produces animations or static images of KEGG pathways by overlaying high-throughput data over handdrawn KEGG pathway maps.

A comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species. KnetMiner is a web application to search and visualise genome-scale knowledge networks. It is used by scientists in academia and industry to accelerate gene-trait discovery research. KnetMiner offers features such as keyword, gene list and genome region search, query refinement, gene ranking, gene set enrichment analysis and interactive visualisation of knowledge networks and genomic information.

This workflow reads images from a high throughput experiment acquired with an Olympus ScanR Microscope. A subset of the image data is used to train a classifier, which is then applied to the whole dataset. A classifier is trained on exemplary images and applied to the whole dataset.

Virtual infrastructure network supporting cooperation between research units 

A Galaxy on-demand service. The platform allows users to configure and deploy private or public Galaxy instances choosing from multiple software and hardware setups.

Access to aRNA research tools for secondary structure prediction, structure alignments, interaction prediction, kinetics etc. Databases and Utils include:

• TRNAdb
• Mitos
• DARIO
• Plexy
• RNAsnoop
• RNAstrand 
• Ryoto

Species focused genome data resource for sea lice, provides a genome browser, access to high-throughput data and LIMS.

A web tool and a mobile app for exploring the entire Tree of Life

LifeSoaks calculates solvent channels and their corresponding bottleneck radii by constructing a three dimensional Voronoi diagram. 

Lipidomics Informatics for Life Sciences (LIFS) provides the bioinformatic framework to understand lipids in context and create an integrative systems biology view for lipid research.

Genomic analyses require flexible models that can be adapted to the needs of the user. Limix is a flexible and efficient linear mixed model library with interfaces to Python.