Integrating heterogeneous sequence information for transcriptome-wide microarray design; a Zebrafish example

BMC Research Notes

Table 2 Characteristics of the Zebrafish Microarray Design

	TC uni-directional	TC 2 bi-directional	Sub-sequences	Vega 37	Ensembl 57	RefSeq 39	UniGene 117
Probe target candidate sequences	97,316	2,303	5,299	22,412	20,728	20,533	41,245
TCs/sequences with 5 probes	3,397	67	0	821	503	935	1,205
TCs/sequences with 4 probes	2,213	139	0	328	199	394	1,431
TCs/sequences with 3 probes	4,015	233	0	714	309	618	2,607
TCs/sequences with 2 probes	8,080	389	1	1,558	676	1,138	5,098
TCs/sequences with 1 probe	23,772	947	23	5,446	2,246	3,049	14,001
TCs/sequences without cross-hybridizing probes	41,477	1,775	24	8,867	3,933	6,134	24,342
TCs/sequences with a cross-hybridizing probe	54,461	484	4,620	13,209	16,330	13,954	16,072
Total queried TCs/sequences	95,938	2,259	4,644	22,076	20,263	20,088	40,414

The rows represent the number of candidate sequences and the design result of OligoPicker [4]. The columns represent the number of TCs in one direction, the number of TCs presented to the oligo-design software as reverse complement, and the number of subsequences. The last four columns show the origin of the sequences on which the probe design has been based.

ISSN: 1756-0500