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

ABSTRACT: 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 wer

SUBMITTER: Premkrishnan BV 

PROVIDER: S-EPMC3313062 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature