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Center director:
Prof. Niels Tommerup
tommerup@imbg.ku.dk







Centre contact information

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Bioinformatics at WJC

WJC offers several online bioinformatics tools. These tools are all developed in-house. Technical questions can be addressed to allan@imbg.ku.dk.

Databases

MCNdb

Mendelian Cytogenetics Network Database version II. Online version is available at http://www.mcndb.org

Multiplex Network Database

Comprehensive database of K+ channel mutation yeast clones. Online version can be found here.

Sequence tools

Oligo sequence scanner

Search the genome, individual chromosomes or your own fasta files for small dna-sequences. Output will be statistics and links to the genome browser or ensemble. You can also get a genome browser track as output. Link: http://seqscan.medgen.ku.dk

Java Tools

This is a collection of tools using Java Web Start which means that you must have java 5.0 or newer installed to use them. Java can be downloaded here. Using this system, you will ble to run the programs locally but automatically get the newest version if you have a network connection.

Simulated bivariate flow karyogram

Simulates flowsorting of chromosomes from a balanced translocation. A short introduction can be found here.

Feature clustering

Different ways to cluster features from a bed-file (eg. UCSC tracks) using user defined parameters. Outputs the results in a bed-file that can be uploaded as a track to UCSC browser

Data Formatter

Used to change tab delimited text-files. The dataformat is changed by various search and replace actions. You can add a prefix or postfix to a certain column, remove lines with specific content etc.

Track Worker

Work with track for the UCSC genome browser.

MirMade

A database with predicted miRNA targets using 6 different methods. The source is annotated 3'UTRs from Ensemble v38. NOTE! Be aware that due to some unknown error it is VERY slow.