Bioinformatics Centre > Services and Software
Services and Software
The Bioinformatics Centre offers a range of free on-line services, open-access databases and open source software packages.
Agene is a fully automated gene predictor for eukaryote. Agene automatically generates a species-specific gene predictor from a set of reliable mRNA sequences and a genome.
A framework for promoter analysis based on a fast search engine using enhanced suffix arrays. The framework includes several statistics for calculating over-representation of motifs in a set of promoters from co-regulated genes compared to a background set.
BARNACLE is a Python library for RNA 3D structure prediction. It can be used for probabilistic sampling of RNA structures that are compatible with a given nucleotide sequence and that are RNA like on a local length scale.
BASILISK is a probabilistic model of the conformational space of amino acid side chains in proteins. Unlike rotamer libraries, BASILISK models the chi angles in continuous space, including the influence of the protein's backbone.
BayesMD is a flexible, fully Bayesian model for motif discovery consisting of motif, background and alignment modules. BayesMD can be customized to different kind of biological applications, e.g. microarray, ChIP-chip, ditag, CAGE data analysis by integrating appropriately chosen features and functionalities.
| EasyGene 1.2
EasyGene is a fully automated gene prediction for prokaryotes. EasyGene produces a list of predicted genes for a chosen prokaryotic genome. EasyGene 1.1 is also available.
GMD is an R package for non-parametric distance measurement between two discrete frequency distributions (histograms), with case studies in clustering of the distributions of high-throughput sequencing reads. The package also facilitate cluster analysis with generic histogram construction, generic distance measure, general evaluation of clustering results by an "elbow" rule and an enhanced "heatmap" visualization.
JASPAR is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors and other proteins interacting with DNA in a sequence-specific manner.
MASTR performs multiple alignment and secondary structure prediction on a set of structural RNA sequences.
miRMaid is an intuitive and modular software platform designed to unify miRBase and independent miRNA data resources. It enables miRNA researchers to computationally address complex questions involving the multitude of miRNA data resources.
| MoAn - Motif Annealer
MoAn is a discriminative pattern finder capable of using a very large negative set to greatly improve its predictive power. It is capable of handling sequences that are not repeat masked given that the negative set is a representative sample of promoters from the organism examined.
Mocapy++ is a Dynamic Bayesian Network toolkit, implemented in C++. It supports discrete, multinomial, Gaussian, Kent, Von Mises and Poisson nodes. Inference and learning is done by Gibbs sampling/Stochastic-EM.
Phaistos is a collection of tools for proteins structure prediction. It currently features the FB5DBN and TorusDBN models, which make it possible to sample protein structures compatible with a given amino acid and/or secondary structure sequence.
Phobius is a server for prediction of transmembrane topology and signal peptides from the amino acid sequence of a protein.
TranCov is a collection of R scripts for calculating coverage in transcriptome experiments. It can be used to assess the complexity of the transcriptome using a number of technologies, e.g. CAGE or RNA-Seq. The two methods implemented are: 1) Generalized inverse Gaussian-Poisson 2) Stick breaking process.
| Saqqaq Genome Project
The primary data from the saqqaq genome project: the sequencing of an Ancient Human Genome, obtained from a permafrost-preserved hair, about 4,000 years old, of a male palaeo-Eskimo of the Saqqaq culture, the earliest known settlers in Greenland.
HemaExplorer is an easy webtool for visualization of gene expression in the hematopoetic system. The webserver takes one or two genes as query and provides plots of the expression of the gene in cells involved in haematopoiesis. Currently the database contains options for the human normal myeloid system, human AML and mouse hematopoietic system.