Software

The lab develops algorithms and tools to process and interpret biological data:

HATSEQ

Reference

We have build a method to analyze your ChIP-array or ChIP-Seq data. The method can accurately detect peak boundaries among different types of experimental data, such as Protein-DNA interactions, Histone modifications, methylated fragments and more! This tool does not require any knowledge about scripting languages because of the friendly graphic user interface (GUI). Install HATSEQ on your PC, MACbook or Unix, select the files to-be-analyzed, and hit the run button. If you also want to know whether motifs or pathways are enriched for the detected regions in your data, simply check the boxes in the GUI. After pressing the Run button in the GUI, we do the job for you! You can grab a cup of coffee.

CytoscapeRPC

Reference

CytoscapeRPC is a plugin for Cytoscape which allows users to create, query and modify Cytoscape networks from any programming language which supports XML-RPC. This enables them to access Cytoscape functionality and visualize their data interactively without leaving the programming environment with which they are familiar.

SPiCE

Reference

We have developed the web-based software tool SPiCE for exploring sequence-based features of proteins in predefined classes. It offers data upload/download, sequence-based feature calculation, data visualization and protein classifier construction and testing in a single integrated, interactive environment. To illustrate its use, two example datasets are included showing the identification of differences in amino acid composition between proteins yielding low and high production levels in fungi and low and high expression levels in yeast, respectively.

IBIDAS

Reference

Ibidas is an environment for data handling and exploration, able to cope with different data structures and sources.

MaRIboES

Reference

Many enzymes are aspecific, or even promiscuous: they can catalyze transformations of more metabolites than the traditional ones as listed in e.g. KEGG. This information is currently only available in databases, such as the BRENDA enzyme activity database. We have developed a method to model enzyme aspecificity, by predicting whether an input compound is likely to be transformed by a certain enzyme. This system, called MaRIboES (metabolite and reaction inference based on enzyme specificities), has many applications, for example to complete reconstructed metabolic networks, to aid in metabolic engineering or to help identify unknown peaks in mass spectra. MaRIboES employs structural and stereochemistry similarity measures and molecular fingerprints to generalise enzymatic reactions based on data available in BRENDA.

MAIA

Reference

MAIA is an algorithm to integrate multiple genome assemblies, for example assemblies originating from different runs of a de novo assembler, assemblies of different data types or comparative assemblies. MAIA produces one .xgmml file per chromosome, which you can visualize in Cytoscape (File > Import > Network).

GRASS

Reference

GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.

The following modules are available:

  • Scaffold optimizer (solves the MIQP optimization problem formulation to produce scaffold nucleotide sequences)
  • Data linker (uses available information sources to derive scaffolding constraints; currently supports paired ends and mate pairs, and reference genomes)

Additionally the following tools are present:

  • Breakpoint counter (assesses scaffold correctness by aligning scaffolds to reference sequences and counting breakpoints)

 

HIPSEC

Reference

Hipsec predicts if gene overexpression of an extracellular protein will lead to successful high-level production in Aspergillus niger. The prediction is based on a protein's amino acid sequence. A fasta file with one or more protein sequences can be pasted into the the text area or uploaded. 

Magnolya

Reference

Magnolya enables copy number variation (CNV) detections without using a reference genome. Magnolya directly compares two next-generation sequencing datasets.

WISECONDOR

Reference

WISECONDOR is a set of python scripts that detects fetal chromosomal and subchromosomal duplications and deletions in maternal blood samples. While other methods usually determine these copy number changes by comparing a test sample with one or more reference samples directly, WISECONDOR bins all reads on all chromosomes and builds a set of reference bins for each target bin by comparing their read depth behavior, and uses these internal reference sets to test for aberrations. This approach allows for stable calls, providing a reliable test for common trisomy cases such as T13, T18, T21, while we were also able to detect T8, T22 and smaller changes on Chr12, Chr13 and Chr18.

MaryGold

Reference

An algorithm for finding and visualising variation within and between metagenome sequence datasets

Proteny

Reference

A tool to analyze synteny at the protein level between two organisms.

We present an algorithm to detect statistically significant clusters of exons between two proteomes. The tool provides algorithms to quickly detect and visualize results in order to support conclusions from genomic data. The method discovers clusters of hits from a bi-directional BLASTp of translated exon sequences in two organisms. A dendrogram for hits is built based on genomic distances between hits, and cut based on significance of a cluster score based on a permutation test at each node in the tree. The result is a set of large clusters describing high exonic conservation.