Skip to main content
Figure 1 | BMC Genomics

Figure 1

From: Defining species specific genome differences in malaria parasites

Figure 1

The overall design schematics of the pan-rodent chip. (A) Methodology of the chip design. Firstly, all possible oligonucleotides of P. yoelii were used to search in the homologous region of the other two species using NCBI blastn and were scored and ranked accordingly. The oligonucleotides were then filtered using three rules such they must have: (i) at least 90% homology to target sequences, (ii) less than 37.5% to non-target sequences and (iii) GC% tolerance of ± 5%. Oligonucleotides for all three species were selected followed by oligonucleotides for P. yoelii and P. berghei and then for P. yoelii and P. chabaudi. Next, the remaining oligonucleotides were selected to be specific for both P. berghei and P. chabaudi. The remaining sequences unaccounted for were then used to design oligonucleotides specific either to P. yoelii, P. berghei or P. chabaudi. (B) Rank-sum strategy. Oligonucleotides were scored accordingly to (i) first and second BLAST hits, (ii) GC content (Tm) and (iii) Smith-Waterman score (self-binding). The oligonucleotides are then ranked based on each parameter and ordinal rank number is given to all oligonucleotides in each parameter rank independently. The final weighted rank-sum (RS) is calculated for all oligonucleotides using multiple weight sets (not indicated) and the lowest value is considered. Finally, the optimal candidate is selected based on the lowest RS(k) amongst all oligonucleotides in the locus of interest [18]

Back to article page