Services

Post-Translational Modifications Mass Spectrometry Calculator (Emerging Service) 

A free web application that simplifies mass spectrometry calculations for post-translationally modified proteins.

Web application for protein-ligand binding sites analysis and visualization | This repositary contains PrankWeb web application.

An ML-based tool/web-server to (i) predict GPCR-G-protein couplings; (ii) visually inspect the protein sequence and structural features that are responsible for a particular coupling; (iii) suggest mutations to rationally design artificial GPCRs with new coupling properties based on predetermined coupling features

Tool for prediction of disease related mutations in proteins. Tool version 2 (PredictSNP 2) for prediction of disease related mutatins within human genome available since 2016.

Primer3 is a program for designing PCR primers and oligos. 

Tool for the detection of structurally similar protein binding sites and pairwise local structural alignment

PROGENy provides a function to infer pathway activity from gene expression. It contains the linear model we inferred in the publication "Perturbation-response genes reveal signalling footprints in cancer gene expression

prolfqua is a comprehensive R package for proteomics differential expression analysis

A complete, flexible analysis of protein microarrays for biomarker discovery. Part of the Proteomics Toolbox. 

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. 

Python package that provides a human-readable formal descriptions of cloning and genetic assembly strategies in Python for simulation and verification.

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.
 

RNA-Seq Analysis Pipeline

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

rawrr is a Bioconductor R package for direct access to Orbitrap data

A tool for analyzing BLAST search output for RNA sequences.

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

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 transcriptome-based breast tumor diagnostic tool

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.

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.