Design and analysis of mismatch probes for long oligonucleotide microarrays

BMC Genomics

Table 2 Comparison of the evenly-distributed MM probes and the MM probes designed using the MPDNN modeling parameter

Name	Type	Sequence*	RSI**
DVU0625_MM4	Evenly	GCAGGCTATAACGACCTGAGGATCCAGGCACGTGAGATGATCCGCAAGGG	0.345
	MPDNN	GCAGGCTATAACGACCTGATAATCCAGACCCGTGAGATAGTCCGCAAGGG	0.109
DVU1466_MM4	Evenly	TGGCAAGGTAGGCGAAGTGGTGGGCGTGAGCACGACGCTGCTGCGTTCTC	0.527
	MPDNN	TGGCAAGGTGGACGAAGTGATAGGCGTAAACACGACGCGACTGCGTTCTC	0.158
DVU1782_MM4	Evenly	GGGTGGGAGGTGGTCTACAACCATCCTGCACTGTATTCCGTCGTCTTGAA	0.190
	MPDNN	GGGTGGGAGAGGGTCTACAACCATCCTGCCCGGTATTCATTCGTCTTGAA	0.100
DVU2526_MM4	Evenly	AAGGTCGAGAAGGTGAACCAGGAACAGATGGTGGAGCATATGGCCCACAG	0.345
	MPDNN	AAGGTCGAGGAAGTGAACCCAGAACAGATAATGGAGCATGTAGCCCACAG	0.136
MMP0707_MM4	Evenly	CAGAGGAGTGGTTCCTGCGACACTTGCGGAAATGATATAAACAAATATTA	0
	MPDNN	CAGAGGAATAGTTCCTGCGACACTTGCGGCAGTGATATGCACAAATATTA	0.100
MMP0926_MM4	Evenly	ATTAAACAGATTAAAGATGATTCAAAATCAAAAGTAAGAGTTAAATCATC	0
	MPDNN	ATTAAACAGGGTAAAGATGATTCAAAATCCGAAGTAAGAAGTAAATCATC	0.042
MMP1559_MM4	Evenly	ATTAAAAGCGGCAATTGGTGAAAAAACATGCCAAGTATCGAGAGTTCCAT	0
	MPDNN	ATTAAAAGATGCAATTGGGAAAAAAACATGCCAAGTATCGAGAGTTCCAT	0.056
SO1362_MM4	Evenly	GGTAGTTATGGTGGGCGGTGAAGGCCAGCGTGGCGGGCTATTTCAACAAA	0.353
	MPDNN	GGTAGTTATAATGGGCGGTAAGGGCCAACTTGGCGGGCGGTTTCAACAAA	0.102
SO1779_MM4	Evenly	CGCATTTCGGTTGGCAACCGTCAACAGGTGAAACAGAAGACATTCAAACT	0
	MPDNN	CGCATTTCGGTTGGCAAACTTCAACAGGTGAAACAGAAAGCATTCAAACT	0.101
SO2452_MM4	Evenly	GTTACATGAATTTGGTGATAGTCAAGATTAGCAGATCCTAATGCAACAAG	0
	MPDNN	GTTACATGACTGTGGTGGTCGTCAAGAGTGGCAGATCCTAATGCAACAAG	0.101

*The 50-mer MM probe sequences. The letters in shadow are the mismatched nucleotides.
**The predicted relative signal intensity (RSI) using the MPDNN model.

ISSN: 1471-2164