Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy

BMC Bioinformatics

Table 1 The comparison of designed oligonucleotides from different programs

Programs*	E. coli K12 (4237 cds)		S. cerevisiae (6680 cds)		P. falciparum (5363 cds)
	#designed^a	#accepted ^b	#designed	#accepted	#designed	#accepted
OligoRankPick	4232 ^ξ	4047(95.6) ^&	6679 ^ζ	6096(91.3)	5363	5092(94.9)
ArrayOligoSelector	4201	3371(80.2)	6221	3471(55.8)	5339	2093(39.2)
OligoPicker	4142	2594(62.6)	6208	3614(58.2)	4235	3543(83.7)
OligoAarray 2.1	3221	2826(87.7)	6587	4440(67.4)	5206	2317(44.5)

*ArrayOligoSelector 3.8.4; OligoPicker; OligoArray 2.1. a: oligonucleotide number selected by the program; b: good oligonucleotide number based on BLAST score of non-target (<= 40% continuous identity) and GC content (± 5%). & Percentage of good quality oligonucleotide to total selected oligonucleotide (in the bracket). ξ Five rejected coding sequences are less than 70 bp. ζ Only one rejected sequence is YJR151W-A (51 bp).

ISSN: 1471-2105