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)
Church lab home page
adnan@genetics.med.harvard.edu
July 2, 1999