Services and Software – Bioinformatics Centre - University of Copenhagen

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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.

ANGSD is a software for analyzing next generation sequencing data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genotype uncertainty into account instead of basing the analysis on called genotypes. This is especially useful for low and medium depth data.
Companion to the paper "MicroRNA transfection and AGO-bound CLIP-seq datasets reveal distinct determinants of miRNA action" and provides predictions for miRNA targets for human and mouse using the two predictive models described in the paper: a model trained from microarray studies following transfection, and a model trained from PAR-CLIP datasets.
Asap logo Asap
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.
The Bayesembler is a Bayesian method for doing transcriptome assembly from RNA-seq data.
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.
BloodSpot logo BloodSpot
BloodSpot is a database that provides gene expression profiles of genes and gene signatures in healthy and malignant hematopoiesis and includes data from both humans and mice.
BWA-PSSM is a probabilistic short read aligner based on the use of position specific scoring matrices (PSSM). Like many of the existing aligners it is fast and sensitive. Unlike most other aligners, however, it also adaptible in the sense that one can direct the alignment based on known biases within the data set. It is coded as a modification of the original BWA alignment program and shares the genome index structure as well as many of the command line options.
cWords is a method used for identification of over-represented words in a set of ranked sequences. By default it is aimed at human miRNA analysis; you give a ranked list of differential expression values of genes across two conditions and it finds words in 3' UTRs of lengths 6 and 7 over-represented in the most regulated genes.
  EasyGene 1.2
EasyGene is a fully automated gene prediction for prokaryotes. EasyGene produces a list of predicted genes for a chosen prokaryotic genome.
Exploration of isoform switches in cancer
For easy and fast exploration of isoform switches in TCGA cancer data we generated three interactive online web-services, which can produce the isoform switch analysis plots for all genes with a isoform switch. To facilitate target exploration the gene can be selected/explored through three different angles:
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.
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.
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.
Kaiju logo Kaiju
Kaiju is a program for the taxonomic assignment of high-throughput sequencing reads from whole-genome sequencing of metagenomic DNA.
MASTR performs multiple alignment and secondary structure prediction on a set of structural RNA sequences.
miRMaid logo miRMaid
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 logo 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 logo Mocapy++
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 logo Phaistos
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 logo Phobius
Phobius is a server for prediction of transmembrane topology and signal peptides from the amino acid sequence of a protein.
Saqqaq logo 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.
spliceR is an R package that allows for classification of full length transcripts generated by RNA-seq assemblers such as Cufflinks. spliceR outputs information about classes of alternative splicing, susceptibility of transcripts to the nonsense mediated decay mechanism (NMD), and provides functions for export of data to the GTF format for viewing in genome browsers, and a few plotting functions.
Webserver for Aligning non-coding RNAs. WAR is an easy-to-use webserver that makes it possible to simultaneously use the best methods for aligning and predicting the consensus secondary structure for a set of non-coding RNA sequences.