1、生物信息学软件,JASPAR ConSite TRANSFAC rVista 2.0 MEME Weblog,PISCES CH-HIT PSIPRED ChEMBL David,转录因子结合位点,转录因子：能够结合在某基因上游特异核苷酸序列上的蛋白质，活化后从胞质转位至胞核，通过识别和结合基因启动子区的顺式作用元件,启动和调控基因表达 转录因子结合位点：转录因子结合位点是转录因子调节基因表达时，与转录因子结合的区域,JASPAR,JASPAR 是收集有关转录因子与DNA 结合位点模体(motif)的最全面的公开的数据库, 该数据库是由哥本哈根大学维护。 JASPAR 数据库中所包含的数据,
2、都经过严格筛选, 有确切的实验依据, 通过计算机辅助软件进行整合识别匹配并用生物学手段进行注释,(1) JASPAR CORE (2) JASPAR CNE (3) JASPAR FAM (4) JASPAR PBM (5) JASPAR PBM_HLH (6) JASPAR PBM_HOMEO,JASPAR_CORE 核心数据库,The JASPAR CORE database contains a curated, non-redundant set of profiles, derived from published collections of experimentally defi
3、ned transcription factor binding sites for eukaryotes. The prime difference to similar resources (TRANSFAC, etc) consist of the open data access, non-redundancy and quality.,JASPAR CNE,JASPAR CNE is a collection of 233 matrix profiles By clustering of overrepresented motifs from human conserved non-
4、coding elements. The biochemical and biological role of most of these patterns is still unknown,如何得到位置矩阵,位置矩阵如何打分,Phylogenetic footprinting,Phylogenetic footprinting is a technique used to identify transcription factor binding sites (TFBS) within a non-coding region of DNA of interest by comparing i
5、t to the orthologous sequence in different species.,同源,若两个或多个结构具有相同的祖先，则称它们同源(Homology) 这里相同的祖先既可以指演化论意义上的祖先，即两个结构由一个共同的祖先演化而来，也可以指发育意义上的祖先，即两个结构由胚胎时期的同一组织发育而来。,直系同源与旁系同源,如果两个基因有着几乎一样的DNA序列，那么它们很可能同源 。,同源序列可分为两种：直系同源(orthology)和旁系同源(paralogy)。 直系同源的序列因物种形成(speciation)而被区分开(separated)：若一个基因原先存在于某个物种，
6、而该物种分化为了两个物种，那么新物种中的基因是直系同源的。 啮齿动物和人类,旁系同源的序列因基因复制(gene duplication)而被区分开(separated)：若生物体中的某个基因被复制了，那么两个副本序列就是旁系同源的。 肌红蛋白(myoglobin)和血红蛋白(hemoglobin)被认为是古老的旁系同源体,ConSite,ConSite is a user-friendly, web-based tool for finding cis-regulatory elements in genomic sequences. Predictions are based on the
7、integration of binding site prediction generated with high-quality transcription factor models and cross-species comparison filtering,By incorporating evolutionary constraints, selectivity is increased by an order of magnitude as compared to single-sequence analysis,TRANSFAC,TRANSFAC数据库是关于转录因子、结合位点和
8、与DNA结合的profiles的数据库。由SITE、GENE、FACTOR、CLASS、MATRIX、CELLS、METHOD和REFERENCE等数据表构成。,Match - 1.0 Public,Match is a weight matrix-based program for predicting transcription factor binding sites (TFBS) in DNA sequences. It uses a library of positional weight matrices from TRANSFAC Public 6.0.,rVista 2.0,A
9、nalyzing novel sequences for the presence of known transcription factor binding sites or their weight matrices produces a huge number of false positive predictions that are randomly and uniformily distributed.,rVista combines database searches with comparative sequence analysis, reducing the number
10、of false positive predictions by 95% while maintaining a high sensitivity of the search,MEME,Motif-based sequence analysis tools 寻找DNA，RNA和蛋白质的共有序列 可以在启动子区域搜寻TFBS的结合位点 可以搜寻蛋白质家族的模体(motif),Weblog,Weblogo基于多序列比对信息，把多序列的保守信息通过图形表示出来。每个logo由一系列碱基（氨基酸）组成，在每一个序列位置上用总高度表示此位置上的序列保守性，用碱基（氨基酸）字母的高度表示出现的频率,PIS
11、CES,序列相似性比对软件进行序列相似性比对蛋白质预测时序列相似性一般选取：25%，40%,CH-HIT,序列相似性比对软件DOS下运行最低的序列相似性为40%,PSIPRED,PSIPRED (Position Specific Iterated PRED) Server是一个预测蛋白质二级结构的服务器,ChEMBL,ChEMBL is a database of bioactive drug-like small molecules.ChEMBL contains 2-D structures, calculated properties (Molecular Weight) and bioactivities ( binding constants, pharmacology).,
