Probe design

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Folding an oligonucleotide The alignment is based on dinucleotides Substitution matrix is based on binding energies an approximation { { { AT TG CT .........................................................................................CG GT TT { { { AT TG CT ........................................................................................CG GT TT . . . . . . . . . . . . . . . . . . . . . . . Dynamic programming: alignment to inverted self . . . . . . Minimal loop size border
Folding a lot of oligos a fast heuristic implementation AT TG CT .........................................................................................CG GT TT AT TG CT ........................................................................................CG GT TT . . . . . . Full dynamic programming calculation for first probe . . . . . . . . . . . . . . . . . Dynamic programming calculation for second etc. probe . . . . . . . Super-alignment matrix . . . . . . . . . . . . . . . . . . . . . . . . Minimal loop size border Last probe
Page 1 and 2: Probe design for microarrays by H.
Page 3 and 4: Probe Type comparisons PCR products
Page 5 and 6: Download OligoWiz and try the sampl
Page 7 and 8: Probe Specificity Hughes et al. 200
Page 9 and 10: Filtering Self Detecting 50 bp BLAS
Page 11 and 12: Similar Affinity for all oligos Ano
Page 13 and 14: Tm distributions for 30’mers and
Page 15: Avoid self annealing oligos Sensiti
Page 19 and 20: Probes With Very Common sub sequenc
Page 21 and 22: Location of Oligo within transcript
Page 23 and 24: Export the probes to a file Export

Probe design

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