BlockLogo: visualization of peptide and sequence motif conservation.
BlockLogo: visualization of peptide and sequence motif conservation.
复制标题
DOI：
10.1016/j.jim.2013.08.014
复制
发表时间：
2013-12-31
影响因子：
2.2
通讯作者：
Brusic, Vladimir
中科院分区：
文献类型：
--
作者：
Olsen, Lars Ronn;Kudahl, Ulrich Johan;Simon, Christian;Sun, Jing;Schoenbach, Christian;Reinherz, Ellis L.;Zhang, Guang Lan;Brusic, Vladimir
关键词：
BlockLogo 是一个网络服务器应用程序，用于通过多序列比对计算块熵来可视化蛋白质和核苷酸片段、连续蛋白质序列基序和不连续序列基序。用户输入包括多序列比对、基序位置的选择、序列类型和输出格式定义。输出具有 BlockLogo 以及序列徽标和主题频率表。我们将 BlockLogo 部署为在线应用程序，并通过显示 T 细胞表位和 B 细胞表位（连续和不连续）可视化的示例展示了其实用性。我们的附加示例显示了结构基序的可视化和分析，这些结构基序确定了肽与 HLA-DR 分子结合的特异性。 BlockLogo 服务器还采用选定的经过实验验证的预测算法，能够即时预测 MHC 与 15 种常见 HLA I 类和 II 类等位基因的结合亲和力，并对来自多个序列比对的不连续表位进行可视化分析。它可以对通常被描述为正则表达式的结构和功能主题进行可视化和分析。它提供了由生物序列中遥远位置组成的不连续基序的紧凑视图。 BlockLogo 位于：http://research4.dfci.harvard.edu/cvc/blocklogo/ 和 http://methilab.bu.edu/blocklogo/
BlockLogo is a web-server application for visualization of protein and nucleotide fragments, continuous protein sequence motifs, and discontinuous sequence motifs using calculation of block entropy from multiple sequence alignments. The user input consists of a multiple sequence alignment, selection of motif positions, type of sequence, and output format definition. The output has BlockLogo along with the sequence logo, and a table of motif frequencies. We deployed BlockLogo as an online application and have demonstrated its utility through examples that show visualization of T-cell epitopes and B-cell epitopes (both continuous and discontinuous). Our additional example shows a visualization and analysis of structural motifs that determine specificity of peptide binding to HLA-DR molecules. The BlockLogo server also employs selected experimentally validated prediction algorithms to enable on-the-fly prediction of MHC binding affinity to 15 common HLA class I and class II alleles as well as visual analysis of discontinuous epitopes from multiple sequence alignments. It enables the visualization and analysis of structural and functional motifs that are usually described as regular expressions. It provides a compact view of discontinuous motifs composed of distant positions within biological sequences. BlockLogo is available at: http://research4.dfci.harvard.edu/cvc/blocklogo/ and http://methilab.bu.edu/blocklogo/
登录
查看更多内容
影响因子：
64.5
作者：
Mahrus S;Trinidad JC;Barkan DT;Sali A;Burlingame AL;Wells JA
通讯作者：
Wells JA
影响因子：
--
作者：
SHANNON, CE
通讯作者：
SHANNON, CE
影响因子：
14.9
作者：
Robinson J;Halliwell JA;McWilliam H;Lopez R;Parham P;Marsh SG
通讯作者：
Marsh SG
影响因子：
32.4
作者：
Sun, Zhen-Yu J.;Oh, Kyoung Joon;Reinherz, Ellis L.
通讯作者：
Reinherz, Ellis L.
影响因子：
14.9
作者：
Thomsen MC;Nielsen M
通讯作者：
Nielsen M