Bioinformatics Vol. 18 no. 11 2002
Pages 1432-1437
© 2002 Oxford University Press
PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis
1 Protein Informatics Group, Life Sciences Division
2 Environmental Sciences Division, Oak Ridge National Laboratory,
Oak Ridge, TN 37831, USA
Received on March 6, 2002
; revised on April 29, 2002
; accepted on May 2, 2002
Motivation: DNA microarray is a powerful high-throughput tool for studying gene function and regulatory networks. Due to the problem of potential cross hybridization, using full-length genes for microarray construction is not appropriate in some situations. A bioinformatic tool, PRIMEGENS, has recently been developed for the automatic design of PCR primers using DNA fragments that are specific to individual open reading frames (ORFs).
Results: PRIMEGENS first carries out a BLAST search for each target ORF against all other ORFs of the genome to quickly identify possible homologous sequences. Then it performs optimal sequence alignment between the target ORF and each of its homologous ORFs using dynamic programming. PRIMEGENS uses the sequence alignments to select gene- specific fragments, and then feeds the fragments to the Primer3 program to design primer pairs for PCR amplification. PRIMEGENS can be run from the command line on Unix/Linux platforms as a stand-alone package or it can be used from a Web interface. The program runs efficiently, and it takes a few seconds per sequence on a typical workstation. PCR primers specific to individual ORFs from Shewanella oneidensis MR-1 and Deinococcus radiodurans R1 have been designed. The PCR amplification results indicate that this method is very efficient and reliable for designing specific probes for microarray analysis.
Availability: The software is available at http://compbio.ornl.gov/structure/primegens/
Contact: xud{at}ornl.gov
* To whom correspondence should be addressed.
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