E. coli cross-hybridization and unique regions

try cross-hyb yourself for specific genes

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 E. coli ORFs were BLASTed against all others, with E=0.001, gaps enabled and low-complexity filtering disabled. The shortest resulting hits were 20/20. Matches to self and to the wrong strand (i.e., not transcribed) were not considered.

ORFs without x-hyb
ORFs with some xhyb but some unique regions (max. unique region >= 50 bases)
ORFs with small or no unique regions (max. unique region < 50 bases)
details: summary of BLAST results


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adnan@genetics.med.harvard.edu

July 1, 1999