Promide: Probe Selection and Microarray Design

Comments about this page are very welcome. Please send them to Sven.Rahmann |at| cebitec.uni-bielefeld.de.

Important Notice: While the Promide software continues to be avialable here, the author has moved to Bielefeld University. The new homepage can be found here.

Promide is a collection of command-line tools for Probe selection and Microarray Design. Promide is currently in beta stage, meaning that it has been debugged and works on most systems. However, some parameters may still need tweaking or optimization.

When you are obtaining any version of Promide, you do so entirely at your own risk.

Promide is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

• Read the Manual
• Read the License Agreement
• Read the NO WARRANTY Statement

To obtain a copy of Promide, make sure you understand and agree to the License Agreement. Then write an e-mail to Sven.Rahmann |at| cebitec.uni-bielefeld.de requesting a license. Please include the following:

1. The names and affiliations of all individuals who will be using the software. The license is strictly personalized. No additional persons may use the software without acquiring a personal license for themselves.
2. The operating system for which you desire the Promide executables. At the moment, we can only provide Linux, OSF1, and SunOs executables.
3. Please FAX a copy of the license agreement to ++49 - 521 - 106-6495 (49 is the country code of Germany; 521 the city code of Bielefeld), in which the names and affiliations of all users are inserted into the appropriate fields.

To use Promide, you need a working installation of PERL, which can be obtained from http://www.cpan.org.

At present, you also need mkvtree, a tool to build enhanced suffix arrays, written by Stefan Kurtz at University of Hamburg. You have to obtain a separate license for mkvtree. Like Promide, it is provided at no cost to academic users. Please visit the vmatch website and contact the author Stefan Kurtz.

		Saccharomyces cerevisiae (budding yeast) Set of 25-mers for all predicted yeast ORFs
		Neurospora crassa (coming soon)
		Arabidopsis thaliana (coming soon)

Important Notes:

• This information is provided "as-is" WITHOUT ANY WARRANTY, either expressed or implied including, but not limited to, the implied warranties of merchantability, fitness for a particular purpose, or non-infringement. The user of this information assumes all risk of its accuracy and for its use.
• The files are gzipped; they were created on a LINUX/UNIX system. Use gunzip -a  to decompress them to ensure correct line breaks (ascii mode).
• The format of the oligo file is described in the manual accompanying the Promide Software.

• Verena Aign. Department of Functional Genome Analysis. Deutsches Krebsforschungszentrum DKFZ (German Cancer Research Center), Heidelberg
• febit AG Mannheim
• If you need a custom set of oligos, please contact me by e-mail, and we shall see what we can do!

1. Sven Rahmann. Fast large scale oligonucleotide selection using the longest common factor approach.  Journal of Bioinform atics and Computational Biology, 1(2):343-361, 2003.
   (This paper presents a fast method to select gene-specific oligos for large-scale datasets, based on an algorithm that uses an enhanced suffix array.)
2. Sven Rahmann. Fast and sensitive probe selection for DNA chips using jumps in matching statistics. In Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference (CSB 2003), pages 57-64. IEEE, 2003.
3. Alexander Schliep, David C. Torney, and Sven Rahmann.  Group testing with DNA chips: Generating designs and decoding experime nts.  In Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference (CSB 2003), pages 84-93. IEEE, 2003.

• The melting temperature computations use the unified parameter set described in: J. SantaLucia. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA 95:1460-1465 (1998)
• A paper by Lars Kaderali and Alexander Schliep takes the approach to find optimal melting temperature alignments of each candidate oligo to every background sequence.  See: Lars Kaderali and Alexander Schliep. Selecting Signature Oligonucleotides to Identify Organisms using DNA Arrays. Bioinformatics 18(10):1340-1349 (2002).
• There is also a paper on oligo selection by Fugen Li and Gary Stormo: Selection of optimal DNA oligos for gene expression arrays. Bioinformatics 2001 17(11):1067-1076.