Software and services
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.
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 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.
| 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:
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 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.
| 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.
| 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.
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.
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Free on-line services available
Open access database available
Open source software available