FAQs
What is PRIMEGENS ?
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 have generated vast amount of sequence data. High-throughput data analysis and its study is one of the primary focuses for molecular biologist. Microarray is one of the most common tools for studying gene expression on a large scale. In cDNA microarray, typically each spot on the array contains sequence segment of a specific gene, which is amplified by PCR. The segment is expected to be gene-specifc to avoid cross hybridization among genes sharing significant sequence identity. In another case, researchers may simply want to amplify gene-specific segments for a selected group of genes using RT-PCR. In both cases, the problem can be formulated to choose a gene-specific segment for a gene in a genome and then design PCR primers according to some specifications. Such an objective is often achieved manually. For example, a user can apply Primer3 for primer design for a given sequence. Primer3 designs many possible primers pair for a given sequence but it does not guarantee their uniqueness in the whole genome. Therefore, a user has to manually run BLAST for each PCR product against the genome to search to avoid cross hybridization. The manual approach cannot be applied to a large scale. PRIMEGENS does not only automates such a process but also automates the primer generation on the large scale. Furthermore, PRIMEGENS has a rigorous formulation, which has a much better chance to find gene specific segment than a manuall process.
Authors and References
PRIMEGENS 1.0 was written by Dong Xu. The updates in the version 2.0, including the graphical user interface, were developed Gyan Prakash Srivastava. If you use PRIMEGENS in any publication, please refer to:
Dong Xu, Guangshan Li, Liyou Wu, Jizhong Zhou and Ying Xu. PRIMEGENS: A Computer Program for Robust and Efficient Design of Gene-Specific Probes for Microarray Analysis. Bioinformatics. 18: 1432 - 1437. 2002.
Bug Reports
Please email any bugs of the program to Gyan Prakash Srivastava.
Copyright / Availability
The program PRIMEGENS 2.0 is developed and distributed by Digital Biology Laboratory, University of Missouri, Columbia. PRIMEGENS executables are free of charge to any users. Source code of PRIMEGENS may be available under research agreement (please contact Dong Xu). Suggestions for development of new features are welcome.
PRIMEGENS incorporates two third-party programs in the public domain, 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.
Acknowledgment
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.
