Predicting Crosshybridization in Microarrays

Until today the algorithms for detection of seg- ments in genes which can cause crosshybridiza- tion are limited, because they solve only one prob- lem. In this work we will try to take into account the importance of similarity through BLASTn (Basic Local Alignment Search Tool nucleotide) and on the other hand, the thermodynamical ef- fect approximated with the Nearest-Neighbour- Theory to forcast the chance of crosshybridiza- tion. By using these two tools we will show how probes which are likely to produce crosshy- bridization can be detected. Then we will show the proposed algorithm on yeast and one of its genes to illustrate the developed process.