ModCRElib：建模顺式调控元件的独立软件包
ModCRElib: a standalone package to model cis -regulatory elements
ModCRElib 是一个独立软件包，用于分析转录因子（TF）与 DNA 的相互作用及调控复合物中的蛋白间相互作用，可基于结构信息预测 TF 结合基序、沿 DNA 序列生成结合亲和力打分谱、预测 TF 结合位点并建模高阶调控复合物结构。该包支持多种输入数据格式与来源，用户既可遵循文档给出的分析流程，也可单独调用其中任一功能，从而以不受限制、可定制的方式使用 ModCRE 服务器提供的服务。
来源：NAR Genomics and Bioinformatics · doi.org
The ModCRElib package provides various tools for the analysis and modelling of transcription factor (TF)-DNA and regulatory complex inter-protein interactions. It takes structural information on these interactions to predict TF-binding motifs, generate binding profiles along DNA sequences that score the binding affinity, predict TF-binding sites, and model the structure of higher order regulatory complexes. It is capable of working with a variety of input data formats and sources. The user may follow the analysis pipeline as outlined in the documentation or the user can make use of any of the multiple functionalities in an isolated manner. The package takes the service offered by the ModCRE server and enables users to apply its tools in an unrestricted and customizable manner. In this paper we provide five example uses of ModCRElib. This includes (i) TF-binding affinity prediction, (ii) TF ensemble pattern of bindings (aggregation of motifs), (iii) characterization of specificity in TF-binding sites along target DNA sequences, (iv) modelling TF bound to predicted binding sites, and (v) the generation of statistical potential derived scoring profiles of TF interacting with DNA.