Bioinformatics @ MolGen	web
Website	Bioinformatics tools developed at the department of Molecular Genetics, RUG, university of Groningen, the Netherlands.
GET License	Projector / Projector 2	Unix
ONLINE version	Projector was designed for automatic positioning of contigs from an unfinished prokaryotic genome on a template genome of a closely related strain or species.
* Projector: automatic contig mapping for gap closure purposes     by Sacha A.F.T. van Hijum*, Aldert L. Zomer, Oscar P. Kuipers, and Jan Kok     Nucleic Acids Research, 2003, Vol. 31, No. 22 e144		Publications
GET License	UniFrag	Unix
ONLINE version	The UniFrag program selects from a list of DNA sequences the unique regions by using the "BlastAll" program. Fragment sizes, overlaps, and many other features can be customized. "UniFrag" creates "GenomePrimer" compatible DNA sequence lists.
* UniFrag and GenomePrimer, programs to select primers for genome-wide production of unique amplicons     by Sacha A.F.T. van Hijum, Anne de Jong*, Girbe Buist, Jan Kok, and Oscar P. Kuipers     Bioinformatics, 2003, Vol. 19, No. 12, 1580-1582		Publications
GET License	Genome2D	MS Windows
	Genome2D visualizes a bacterial genome with all its individual genes on a single computer screen genome enables quick identification of biologically relevant information such as gene orientation, operon structure, transcriptional terminators or regulator binding sites. Using a simple input file subsets of genes can be visualized by single or multiple coloring or by a color gradient when values are used. The input file is a tab-delimited text file, comprising one column with the genes to be colored and one column indicating their colors or a value. When applied to DNA microarray data the values could represent differences in transcription levels. This feature enables easy and rapid identification of genes that are transcriptionally linked. In a multiple transcriptome analysis experiment, e.g. a measurement in time, all data sets can be loaded as separate input files and subsequently shown in animation. Thus, the changes in gene expression can be readily recognised. In addition, Genome2D contains a toolbox of bioinformatics utilities such as:   Convert gene lists (tab-delimited text files) to FastA format. BLAST at a location of choice : local, NCBI, etc. Search in the genome for binding sites of transcriptional regulators ,with or without a trained set Calculate the codon usage in a complete genome or a subset of genes Randomise the genome for statistical purposes - gene fragments or single basepairs Extract non-coding regions from a genome
* Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data.     by Baerends R. J., Smits, W. K., de Jong, A., Hamoen, L. W., Kok, J. and Kuipers, O. P.     (2004) Genome Biol., 5, R37		Publications
GET License	GenomePrimer	MS Windows
	GenomePrimeris a program that provides a high-throughput method to select, with minimal user intervention and maximum flexibility, the most unique regions within DNA sequences and design primers that meet certain preset criteria. In the Molecular Genetics group, GenomePrimer has been successfully used to design amplicon primers for DNA microarrays of several Gram-positive bacteria, namely   Lactococcus lactis IL1403 Lactococcus lactis MG1363 Streptococcus pneumoniae TIGR4 Lactobacillus plantarum WCFS1
* UniFrag and GenomePrimer, programs to select primers for genome-wide production of unique amplicons     by Sacha A.F.T. van Hijum, Anne de Jong*, Girbe Buist, Jan Kok, and Oscar P. Kuipers     Bioinformatics, 2003, Vol. 19, No. 12, 1580-1582		Publications
GET License	MicroPreP	MS Windows
	The user-friendly MicroPreP framework was developed to transform raw intensity data from cDNA microarrays into high-quality data. The main features of this software are: Lowess normalization; merging of DNA microarray data from changing slide versions; outlier detection; and slide quality assessment.
* MicroPreP: a cDNA microarray data pre-processing framework     by Sacha A.F.T. van Hijum*, Jorge Garcia de la Nava, Oswaldo Trelles, Jan Kok, and Oscar P. Kuipers     Applied Bioinformatics 2003, Vol. 2, 241-244.		Publications