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Comparative and Functional Genomics
Volume 2012, Article ID 913709, 5 pages
Research Article

In Silico RAPD Priming Sites in Expressed Sequences and iSCAR Markers for Oil Palm

1Department of Computational Biology & Bioinformatics, North Campus-Kariavattom, University of Kerala, Thiruvananthapuram, Kerala 695581, India
2Horticulture Section, ICAR Research Complex for Goa, Ela Old Goa 403402, India

Received 26 August 2011; Revised 8 November 2011; Accepted 4 January 2012

Academic Editor: Brian Wigdahl

Copyright © 2012 Balakrishnan Vasanthakumari Premkrishnan and Vadivel Arunachalam. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


RAPD is a simple dominant marker system widely used in biology. Effectiveness of RAPD can be improved by selecting and redesigning primers whose priming sites occur in target sequence(s) of gene or organism at optimum distance. We developed software that uses sequences of random decamer primers and nucleotide sequence(s) as two input files. It locates the priming sites in input sequences and generates output files listing frequency and distance between priming sites. When the priming sites of a single primer occur more than once in a sequence with a distance of 200 to 2000 bp, the software also designs pairs of iSCAR primers. An input of 387 RAPD primers and 42,432 expressed sequences of oil palm are used as test. Wet-lab PCR results from a publication that used the same set of primers were compared with software output on priming sites. In the test sequences of oil palm covering 1.4% of genome, we found that at least 60% the primers chosen using software are sure of giving PCR amplification. We designed 641 iSCAR primers suitable for amplification of oil palm DNA. The software successfully predicted 92% (67 out of 73) of published polymorphic RAPD primers in oil palm.