Abstract
To know the regulation of gene transcription, transcription factor binding sites (motifs) are helpful information. In fact, cDNA microarray hybridization (ChIP array) has became a popular tool for recognizing motif from gene sequences. However the ChIp array can only map the probable sequence within 1-2 kilobases resolution. Our goal is to find out the motif binding site without the information of motif length. To reach this goal we design a computational program, base on the discriminator and binomial model to find the most possible patterns. And we compare our performance to the program called constraint-less Cosmo [1]. From the simulation results, we can prove that our program is better than Cosmo.