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Bioinformatics Tools |
♦ ♦ ♦ Our compute cluster is at best intermittently available at the moment. All tools (including Domaination, NatalieQ, NGS-eval, Praline, PRC, Serendip, and Sympred) may therefore be down.
Given the advanced age of the cluster hardware, we cannot currently guarantee its continued availability. We are working on a replacement solution.
Please contact us if you have questions.
Our apologies for any inconveniences caused.
♦ ♦ ♦
♣ 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 PhyloPars PhyloPars takes an incomplete feature matrix and a phylogeny as input and estimates the missing parameter values
♣ 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 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 SeRenDIP Predict protein-protein interaction sites from sequence 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 2.0FluxEs 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.
♣ Next Generation Sequencing TaxMan Calculate taxonomic coverage of your 16S rDNA primers in silico NGS-eval NGS Error analysis and VAriant detection tooL
♣ Downloads You can download bioinformatics software, source codes and substitution matrices, produced by the IBIVU Centre
♣ Compute Cluster Status
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