QPS -二次规划采样器，使用生物物理建模的基序发现器
QPS -- quadratic programming sampler, a motif finder using biophysical modeling
摘要：
我们提出了一个马尔可夫链蒙特卡罗算法的核苷酸序列的局部比对，旨在推断推定的转录因子结合位点，被称为二次规划采样。新的基序发现者结合了转录因子结合位点识别的详细生物物理建模，其产生了将推定的结合位点与其他/背景序列区分开的内在阈值。我们验证的主要功能的算法上的一个样本的四个启动子区从大肠杆菌。所得到的基序描述可以容易地在全基因组上进行评估，以鉴定新的推定结合位点。
英文摘要：
We present a Markov chain Monte Carlo algorithm for local alignments of nucleotide sequences aiming to infer putative transcription factor binding sites, referred to as the quadratic programming sampler. The new motif finder incorporates detailed biophysical modeling of the transcription factor binding site recognition which arises an intrinsic threshold discriminating putative binding sites from other/background sequences. We validate the principal functioning of the algorithm on a sample of four promoter regions from Escherichia coli. The resulting description of the motif can be readily evaluated on the whole genome to identify new putative binding sites.
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