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Bioinformatics Tools

Contents
Multiple Sequence Analysis Pairwise Sequence Alignment Phylogeny Databases & Matrices Array Data Analysis Downloads
Protein Secondary Structure Prediction Protein Analysis RNA Metabolic Flux Estimation Compute cluster status

Multiple Sequence Analysis
PRALINE Multiple sequence alignment toolkit with several strategies to optimise alignment quality
VerAlign Compare a test alignment against a reference alignment on the basis of Column and Sum-of-Pairs score assessment
ConvertAlign Convert your alignment to other formats
Multi-Harmony
Detection of subfamily specific functional sites by combining the new multi-group Sequence Harmony and multi-RELIEF

Pairwise Sequence Alignment
ALICAO Contact-based sequence alignment between query sequence (unknown structure) and template sequence (known structure)
AuberGene A genome alignment program which explores the idea of transitivity of local alignments

Phylogeny / Taxonomy
PhyloPars PhyloPars takes an incomplete feature matrix and a phylogeny as input and estimates the missing parameter values
TaxMan Calculate taxonomic coverage of your 16S rDNA primers in silico

Databases & Matrices
CAO Contact-based substitution matrices
LinkerDB Database for searching and visualising protein inter-domain linkers

Array Data Analysis
aCGH-smooth A "smoothing" algorithm that adjusts the observed array-CGH values such that they represent the copy number of the most common tumor cells
CGHnormaliter Normalization of dual-channel aCGH data displaying imbalanced aberrations
MaRe Microarray Retriever (MaRe) enables batch retrieval from GEO and ArrayExpress microarray repositories
Fuzzy clustering Fuzzy clustering of array CGH data, taking overlapping clusters and outliers into account
Protein Secondary Structure Prediction
YASPIN HMM based neural network secondary structure prediction using PSI-BLAST PSSM matrices
SymPRED Consensus secondary structure prediction using dynamic programming for optimal segmentation or majority voting

Protein Analysis
NatalieQ Query a protein-protein interaction network
DOMAIN3D Identifies globular domains in protein structure
DOMAINATION Domain prediction based on sequence similarity searching
SCOOBY-DOmain Domain prediction based on protein sequence
webPRC The Profile Comparer for alignment-based searching of public domain databases
REPRO Identifies protein sequence repeats using a graph-based iterative clustering procedure
TRUST Repeats detection analysis
SEQATOMS Visualizes all "missing" regions in PDB

RNA
K2N From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal
SPuNC Structure Prediction using Nucleotide Composition

Metabolic Flux Estimation
FluxEs 1.0

FluxEs 2.0
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.

Downloads
You can download bioinformatics software, source codes and substitution matrices, produced by the IBIVU Centre

Compute Cluster Status
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