Berezikov Eugene, Guryev Victor, Cuppen Edwin
Hubrecht Laboratory.
Methods Mol Biol. 2007;395:437-48. doi: 10.1007/978-1-59745-514-5_27.
Prediction of transcription factor binding sites (TFBS) is commonly used to formulate working hypotheses for experimental studies on gene regulation. Computational identification of functional TFBS is complicated because of short length and degeneracy of sequence motifs recognized by transcription factors. Information on conservation of predicted sites in orthologous sequences from different species (phylogenetic footprinting) can be used to distinguish potentially functional elements from background predictions. Results of phylogenetic footprinting may substantially depend on the algorithm used to construct an alignment of orthologous sequences, from which conservation of predicted TFBS is estimated. The CONREAL web server allows prediction and comparison of conserved TFBS based on AVID, BLASTZ, CONREAL, and LAGAN alignments. The web tool is particularly suited for the analysis of individual genes or genomic regions, although the underlying algorithm can also be used in high-throughput promoter analysis.
转录因子结合位点（TFBS）的预测通常用于为基因调控的实验研究制定可行的假设。由于转录因子识别的序列基序长度较短且具有简并性，功能性TFBS的计算识别较为复杂。来自不同物种的直系同源序列中预测位点的保守性信息（系统发育足迹法）可用于从背景预测中区分潜在的功能元件。系统发育足迹法的结果可能在很大程度上取决于用于构建直系同源序列比对的算法，通过该比对来估计预测TFBS的保守性。CONREAL网络服务器允许基于AVID、BLASTZ、CONREAL和LAGAN比对来预测和比较保守的TFBS。该网络工具特别适用于单个基因或基因组区域的分析，尽管其基础算法也可用于高通量启动子分析。
