Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis

Table 3 Performance comparison for 70-mer RGI.

Procedure	Sensitivity factor	rate (%)^a	Cross homology^b	Execution time (hours)
IAB^c for HGI^d	0.2	99	0.53	0.09
	0.3	99	0.53	0.11
IAB for RGI^e	0.2	99	0.53	0.10
	0.3	99	0.53	0.12
Pure BLAST		99	0.58	0.87
BLAST with U_d^f		99	0.53	0.24

^aThe success rate is the percentage of tentative human consensus sequences on which the procedure can find the specific oligo (where the cross homology is less than the threshold). ^bThe cross homology of a specific oligo is determined by the similarity between the specific oligo and its best homology in the non-target sequence. ^cIAB, integration of artificial neural network (ANN) and basic local alignment search tool (BLAST).^dHGI, human gene index.
^eRGI, rat gene index. ^fBLAST with U_d, BLAST search with the density of unique subsequences.

ISSN: 1471-2105