Welcome to SCAMPI

Welcome to SCAMPI a tool for SNPs, CAPS, Microsatellites and Primer Identification. SCAMPI is designed to rapidly detect molecular markers in silico through sequence comparison.

For this purpose, it identifies SNPs as well as InDels between a species reference sequence and any sequenced DNA fragment yielded from another ecotype of this organism after their sequence alignment using BLAST. They are the most common types of intra-specific sequence polymorphisms and thus they are rich resources for the creation of CAPS marker for genotyping. Because CAPS markers use polymorphisms in restriction endonuclease digestion patterns, the sequences are computationally ’digested’ using known sequence patterns of restriction enzyme’s recognition sites. In addition, perfect and approximative repeat polymorphisms (micro- and minisatellites) can be identified using TRED which also can be used as markers. Because both kinds of markers are based on PCR, SCAMPI further enables the directly design of primers near the yielded polymorphic sites using Primer3.

The workflow of SCAMPI for molecular marker detection.


SCAMPI is build as a master thesis project at Chair for Computational Biology (Center for Bioinformatics) at Saarland University, Saarbrücken, Germany. SCAMPI ist still under active development!

SCAMPI is developed by Susanne Pfeifer based on Java, Struts 2, Apache Tomcat and PostgreSQL as key technologies. It utilizes the following free licensed and available software:

We wish to thank all this tools authors for providing their wonderful software freely available to the world. As soon as SCAMPI reaches a mature stability it will also be released under a free software license.


GPL Version 3 This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License Version 3 as published by the Free Software Foundation.

The incorporated third party tools have different licenses. Please see the projects homepages or source code for their terms and conditions.

Download SCAMPI

SCAMPI is not yet released to the public. If you are interested in downloading SCAMPI, please get in touch with us!


Responsible for this content is Susanne Pfeifer, Zum Turm 4, 66583 Spiesen-Elversberg, Germany.
For contact please use scampi <at> susannepfeifer dot de

© 2007-2008 Susanne Pfeifer - All rights reserved.