Multiple Sequence Analysis

Multiple sequence alignment toolkit with several strategies to optimize alignment quality

Compare a test alignment against a reference alignment on the basis of Column and Sum-of-Pairs score assessment

Convert your alignment to other formats

Detection of subfamily specific functional sites by combining the new multi-group Sequence Harmony and multi-RELIEF

Protein Secondary Structure Prediction

HMM based neural network secondary structure prediction using PSI-BLAST PSSM matrices

Consensus secondary structure prediction using dynamic programming for optimal segmentation or majority voting

Protein Analysis

Predict protein-protein interaction sites from sequence using RF models

Predict protein-protein interaction sites from sequence using Neural Net models

Query a protein-protein interaction network

Identifies globular domains in protein structure

Domain prediction based on sequence similarity searching

The Profile Comparer for alignment-based searching of public domain databases

Identifies protein sequence repeats using a graph-based iterative clustering procedure

Repeats detection analysis

Visualizes all “missing” regions in PDB

Pairwise Sequence Alignment

Contact-based sequence alignment between query sequence (unknown structure) and template sequence (known structure)

A genome alignment program which explores the idea of transitivity of local alignments


PhyloPars takes an incomplete feature matrix and a phylogeny as input and estimates the missing parameter values

Databases & Matrices


Contact-based substitution matrices

Database for searching and visualising protein inter-domain linkers

Next Generation Sequencing

Calculate taxonomic coverage of your 16S rDNA primers in silico

NGS Error analysis and VAriant detection tooL



From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal

Structure Prediction using Nucleotide Composition

Metabolic Flux Estimation

FluxEs is a program for metabolic flux analysis using NMR spectra of tracer experiments. FluxEs 1.0 is freely available via a web interface. FluxEs 2.0 is a development version and is available upon request.

Array Data Analysis

Normalization of dual-channel aCGH data displaying imbalanced aberrations

Fuzzy clustering of array CGH data, taking overlapping clusters and outliers into account