Tools
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
Multi‑HarmonyDetection 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
PIPENNPredict protein-protein interaction sites from sequence using Neural Net models with Embedding features
Predict protein-protein interaction sites from sequence using Neural Net models
SeRenDIPPredict protein-protein interaction sites from sequence using RF 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
ALICAOContact-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
Phylogeny
PhyloParsPhyloPars 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
RNA
K2NFrom knotted to nested RNA structures: a variety of computational methods for pseudoknot removal
SPuNCStructure 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