Protein Informatics Group
Home People Research Publications News

Primegens Version 1.0:
Web Server
Server Help


PRIMEGENS (PRIMEr Design Using GEN Specific Fragments) is a computer program to select gene-specific fragments and then design primer pairs for PCR amplifications.

Various genome-scale sequencing projects create vast amount of genomic data. The next key step is to define the function of each gene. One of the powerful tools to investigate gene function is DNA microarray, which is based on DNA-DNA hybridization at high throughput mode. If there is a certain degree of DNA sequence similarity between two genes, both of them may give hybridization signal with the same probe on a microarray. In this case, it is difficult to assign functions for them according to array data. To target a particular gene, it is necessary to design a gene-specific probe, i.e., a segment of a sequence that does not have high sequence similarity to any other sequence in the sequence pool. Traditionally this task is carried out manually through visually checking the output of sequence alignments. It takes a long time for researchers and the results may not be reliable. We have developed PRIMEGENS that solves this problem reliably and efficiently. This program is useful in selecting gene-specific fragments and designing primer pairs for PCR amplification.


If you use PRIMEGENS in any publication, please refer to:

Dong Xu, Ying Xu, Gary Li, and Jizhong Zhou. (2000) A Computer Program for Generating Gene-Specific Fragments for Microarrays. In "Currents in Computational Molecular Biology", edited by S. Miyano, R. Shamir and T. Takagi. Universal Academy Press, Inc. Tokyo, Japan. pages 3-4.

Bug Reports

Please email any bugs of the program to Dong Xu.

Copyright / Availability

The program PRIMEGENS is copyrighted and is NOT in the public domain. PRIMEGENS is free of charge to academic users. If you like to get a copy of executable, please contact us.

PRIMEGENS uses some results from two third-party programs, i.e., Primer3 developed by the Whitehead Institute for Biomedical Research and BLAST developed by National Center for Biotechnology Information (NCBI).

The authors of PRIMEGENS make no representations about the suitability of the software for any purpose. It is provided "as is" without express or implied warranty. The authors shall not be liable for any damages suffered by Licensee from the use of this software.


The development of PRIMEGENS was sponsored by the Office of Biological and Environmental Research, U.S. Department of Energy, under Contract DE-AC05-00OR22725, managed by UT-Battelle, LLC. Dong Xu, Gary Li, Liyou Wu, Jizhong Zhou, and Ying Xu at Oak Ridge National Laboratory are involved in this project. We would like to thank our colleagues Manesh Shah, Joel A. Klappenbach, and Julia Stair for their help and insightful comments.

Life Sciences Division  -  ORNL  -  Disclaimer  -  Webmaster