Service list

An algorithm suite combining Protein Spectrum Matches from different experiments / search engines for consistent, comparable results. Part of the Proteomics Toolbox. 

 ProteinsPlus support life scientists in working with protein structures, and focuses on protein-ligand interactions. The server provides support for the initial steps when dealing with protein structures, namely structure search, quality assessment, and preprocessing. Advanced options, such as protein pocket detection, ensemble generation or prediction of metal coordinations are supported. 

ProteoSign: an end-user online differential proteomics statistical analysis platform

Protoss is a fully automated hydrogen prediction tool for protein-ligand complexes. 

A software tool for the identification of common transcription factors that are likely to regulate a user defined set of genes. PscanChIP is the extension of Pscan to process ChIP-Seq enriched regions.

The PSIPRED Protein Structure Analysis Workbench aggregates several UCL Bioinformatics Group prediction methods into one location. 

A PyMOL plugin, designed to act as simple and intuitive interface between PyMOL and several bioinformatics tools.

Importing and analysing Mass Spec. data in a range of formats and for protein identification.
 

Container cloud, registry and interface. 

RNA-Seq Analysis Pipeline

A cloud computing web application implementing a complete and modular RNA-Seq analysis workflow.

A tool for analyzing BLAST search output for RNA sequences.

The ELIXIR Research Data Management Kit (RDMkit) is an online guide containing best practices in data management applicable to research projects from the beginning to the end. RDMkit is developed and managed by people who work every day with life science data. 

An open-source, curated and peer reviewed pathway database. Its goal is to provide tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling and systems biology.

Exploring and evaluating NGS data utilizing a modular programming structure allowing easy plugins.

A capacity building and training programme in data management for the life sciences

REALPHY - The Reference sequence Alignment based Phylogeny builder is a free online pipeline that can infer phylogenetic trees from whole genome sequence data. The user only has to provide genome sequences in FASTA, GenBank or FASTQ formats. From these sequences phylogenetic trees are inferred via PhyML. The alignments, tree files and information on SNPs and deleted sites are available for download after the analysis is finished.

A PaaS based dashboard to instantiate complex cluster of services in the ReCaS-Bari data center

A transcriptome-based breast tumor diagnostic tool

A database annotating organellar RNA editing processes in their biological context.

A database of RNA editing events in humans from RNA-Seq and DNA-Seq data.

Python scripts developed with the aim to study RNA editing at genomic scale by next generation sequencing data.

Redundans is a pipeline that assists the assembly of heterozygous genomes. It takes as input assembled contigs, sequencing libraries and/or reference sequence and returns scaffolded homozygous genome assembly. 

ReferenceSeeker determines closely-related reference genomes following a scalable hierarchical approach. It combines a fast kmer profile-based database lookup of candidate reference genomes and subsequent computation of specific average nucleotide identity (ANI) values.

Tools to analyse cis-regulatory elements in genome sequences

Set of tools and a web server for complex characterization of repetitive DNA based on data from next generation of sequence reads.

A database of annotated tandem repeat protein structures, combining computer-based methods and manual curation.

The REPET package integrates bioinformatics pipelines dedicated to detecte, annotate and analyse transposable elements (TEs) in genomic sequences. The main pipelines are (i) TEdenovo, which search for interspersed repeats, build consensus sequences and classify them according to TE features, and (ii) TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations exported into GFF3 files.

A tool that can be used to manage researchers’ access rights to bioinformatics databases.

REXdb: a reference database of transposable element protein domains

The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs).