S. cerevisiae cross-hybridization and unique regions

One of the challenges in measuring mRNA levels on microarrays is that genes can cross-hybridize, depending on whether the probes target unique or common regions. In order to predict these events and find unique regions, all S. cerevisiae ORFs were BLASTed against all others, with E=1E-5, gaps enabled and low-complexity filtering disabled. The shortest resulting hits were 24/24. Matches to self and to the wrong strand (i.e., not transcribed) were not considered. A minimum of 50 bases was required for unique regions.

ORFs without x-hyb (4937/6242=79%)
ORFs with some xhyb but some unique regions (max. unique region >= 50 bases) (970/6242=16%)
ORFs with small or no unique regions (max. unique region < 50 bases) (335/6242=5%)
details: summary of BLAST results

PCR primers to amplify unique fragments within ORFs that otherwise cross-hyb (842/970)

PCR primers for miscellaneous ORFs (10)

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adnan@genetics.med.harvard.edu

July 2, 1999