Services: Software Tools

Aligns contigs from a draft genome to a closely related genome, and resolves their relative orientation based on this alignment.

OPASI is a software application for simulation and analysis of biochemical networks and their dynamics.

Galaxy server allowing to align complete assemblies of SARS-CoV-2 genomes with the reference genomic sequence to obtain a list of polymorphic positions and to annotate genetic variants.

Template-based predictor of RNA secondary structure. It takes a template RNA secondary structure(s) and a query RNA sequence(s) and generates secondary structure of the query sequence(s) using the provided structure(s) as a template(s). Biological reliability of the generated structures is evaluated in form of z-scores.

CRISPRCas++ is a new website holding a program called CRISPRCasFinder to detect CRISPR arrays and cas genes in the genome of prokaryotes. CRISPRCasMeta is adapted to the analysis of large metagenomic data. The programs are available online or can be downloaded for local usage. A database called CRISPRCasdb, the successor of CRISPRdb, is accessible on the CRISPRCas++ website. It can be browsed and queried in search for repeat and spacer sequences. 

Chipster is a user-friendly analysis software for high-throughput data. It contains hundreds of analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. 

Curare is a free analysis pipeline for reproducible, high-throughput, bacterial RNA-Seq experiments. Define standardized pipelines customised for your specific workflow, without installing all the tools by yourself.

a web application that provides a graphical interface for Seurat version 2, a popular single-cell RNA-seq (scRNA-seq) package for R. It provides an easy-to-use UI and the ability to export results as an HTML file.

Domain based ANnotation of Transposable Elements (DANTE) uses database of Viridiplantae (Metazoa in progress) protein domains derived from transposable elements (Neumann at al 2019) Domains searching is accomplished engaging LASTAL alignment tool. Domains are subsequently annotated and classified using phylogenetic approach.

Research data management platform to enable researchers to produce FAIR data by design  

System for identification of alterations using protein mass spectrometry.

Prediction of protein sub-mitochondrial localization.

Prediction of secretory signal peptides and cleavage sites in proteins.

DELLY discovers germline and somatic structural variants in short-read massively parallel sequencing data

DESeq2 is an R/Bioconductor package for differential expression analysis of high-throughput sequencing assays (incl. RNA-seq, ChIP-Seq, 4C-Seq, ribosome profiling, CLIP, metagenomics, HT-CRISPR screens) based on the Gamma-Poisson distribution. Part of the Human Omics Analysis Toolbox

An R-package used to extract disease-perturbed subpathways within a pathway network as recorded by RNA-seq experiments.

DEXSeq is an extension of DESeq for the analysis of alternative exon usage. DESeq2 is an R/Bioconductor package for differential expression analysis of high-throughput sequencing assays (incl. RNA-seq, ChIP-Seq, 4C-Seq, ribosome profiling, CLIP, metagenomics, HT-CRISPR screens) based on the Gamma-Poisson distribution. Part of the Human Omics Analysis Toolbox

OpenMS tool for targeted assay generation in metabolomics.

DIANA-LncBase provides an extensive collection of experimentally and on silico predicted miRNA:lncRNA interactions.

DIANA-microT web server is dedicated to miRNA target prediction and functional analysis and is widely used since 2009 from the scientific community. 

DIANA-mirExTra v2.0 performs a combined Differential Expression Analysis (DEA) of mRNAs and microRNAs (miRNAs) to uncover miRNAs and transcription factors (TFs) playing important regulatory roles between two investigated states.

DIANA-miRGen v3.0 provides accurate cell-line-specific miRNA gene transcription start sites (TSSs), coupled with genome-wide maps of transcription factor (TF) binding sites in order to unveil the mechanisms of miRNA transcription regulation.

DIANA-miRPath v3.0 is an online software suite dedicated to the assessment of miRNA regulatory roles and the identification of controlled pathways

OpenMS workflow for Data Independent Acquisition MS and statistical post-analysis.

Web interface for assignment and analysis of DNA conformers.

DoGSite is a grid-based method which uses a Difference of Gaussian filter to detect potential protein binding pockets - solely based on the 3D structure of the macromolecules.

Dorothea contains human and mouse TF regulons. The human regulons were curated and collected from different types of evidence such as literature curated resources, ChIP-seq peaks, TF binding site motifs and interactions inferred directly from gene expression. The mouse regulons were constructed by mapping the human gene symbols to their orthologs in mice. Those regulons can be coupled with any statistical method that aims to analyse gene sets to infer TF activity from gene expression data. Preferably the statistical method viper is used.

This resource includes sequence pipeline (TarO) analysis, a secondary prediction (JPred) structure server, and a protein kinase database and kinase classification pipeline (Kinomer).

A bioinformatics tool for hypothesis generation and prioritization of drugs capable of modulating immune cell activity from transcriptomics data.

Tool to predict backbone dynamics from a single protein sequence