Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization.

ABSTRACT: DNA microarray measurements are susceptible to error caused by non-specific hybridization between a probe and a target (cross-hybridization), or between two targets (bulk-hybridization). Search algorithms such as BLASTN can quickly identify potentially hybridizing sequences. We set out to improve BLASTN accuracy by modifying the substitution matrix and gap penalties. We generated gene expression microarray data for samples in which 1 or 10% of the target mass was an exogenous spike of known sequence. We found that the 10% spike induced 2-fold intensity changes in 3% of the probes, two-third of which were decreases in intensity likely caused by bulk-hybridization. These changes were correlated with similarity between the spike and probe sequences. Interestingly, even very weak similarities

SUBMITTER: Eklund AC 

PROVIDER: S-EPMC2831327 | biostudies-literature | 2010 Mar

REPOSITORIES: biostudies-literature