Probe design

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Mapping Regions 5’ without similarity to other transcripts The Sequence we want to <strong>design</strong> a probe for 50 bp Regions suitable for probes 3’ BLAST hits >75% & longer than 15bp
Filtering Self Detecting 50 bp BLAST hits out The Sequence we want to <strong>design</strong> a oligo for 5’ 3’ Sequence identical or very similar to the query sequence Therefore no BLAST hits with homology > 97% and with a ‘hit length vs. query length’ ratio > 0.8, are considered. BLAST hits >75% & longer than 15bp
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: Probe Specificity Hughes et al. 200
Page 11 and 12: Similar Affinity for all oligos Ano
Page 13 and 14: Tm distributions for 30’mers and
Page 15 and 16: Avoid self annealing oligos Sensiti
Page 17 and 18: Folding a lot of oligos a fast heur
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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