title: ZB/SBS-NTU Plasmodium chabaudi chabaudi 4K v1.0
status: Public on Jun 01 2012
contact.city: Singapore
contact.first: Peter
contact.last: Preiser
contact.email: prpreiser@ntu.edu.sg
contact.address: 60 Nanyang Drive, School of Biological Sciences
contact.country: Singapore
contact.institute: Nanyang Technological University, School of Biological Sciences
organism: Plasmodium chabaudi chabaudi
manufacture_protocol: Modified protocol as described by Hu et al, 2007.
  Since Plasmodium yoelii is the only RMP with a published draft genome, we first designed oligonucleotides against the predicted Plasmodium yoelii gene models. Next, all possible oligonucleotides of Plasmodium yoelii were used to query the homologous regions of the other two rodent malaria parasite species. Next, four parameters were used to select for the best oligonucleotide, namely: BLAST scores (first and second hit), GC content, sequence complexity and self-annealing scores. Each score is then transformed into a rank and a weighted rank-sum is calculated for each oligonucleotide with the final oligonucleotide being selected based on the smallest rank-sum value. These oligonucleotides were then selected to be optimal for all three species, followed by oligonucleotides for Plasmodium yoelii and Plasmodium berghei and then for Plasmodium yoelii and Plasmodium chabaudi. For the remaining predicted open reading frames oligonucleotides specific for each species were then designed.
  References:
  Hu G, Llinas M, Li J, Preiser PR, Bozdech Z: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350.