A subspace method for the detection of transcription factor binding sites

作者：Pairo Erola^*; Maynou Joan; Marco Santiago; Perera Alexandre

来源：Bioinformatics, 2012, 28(10): 1328-1335.

DOI：10.1093/bioinformatics/bts147

Results: In this article, we introduce a novel motif finding method which constructs a subspace based on the covariance of numerical DNA sequences. When a candidate sequence is projected into the modeled subspace, a threshold in the Q-residuals confidence allows us to predict whether this sequence is a binding site. Using the TRANSFAC and JASPAR databases, we compared our Q-residuals detector with existing PSSM methods. In most of the studied TF binding sites, the Q-residuals detector performs significantly better and faster than MATCH and MAST. As compared with Motifscan, a method which takes into account interdependences, the performance of the Q-residuals detector is better when the number of available sequences is small.

• 出版日期2012-5-15