PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information.
PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information.
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DOI：
10.1093/nar/gki390
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发表时间：
2005-07-01
影响因子：
14.9
通讯作者：
Heringa J
中科院分区：
文献类型：
--
作者：
Simossis VA;Heringa J
PRofile ALIgNEment（PRALINE）是一个完全可定制的多序列比对应用程序。除了一些可用的比对策略，PRALINE可以整合来自数据库同源性搜索的信息，以生成同源性扩展的多重比对。PRALINE还提供了七种不同的二级结构预测程序，可以单独使用或组合使用，作为将结构信息整合到比对过程中的共识。该程序可以通过两个单独的接口使用：一个是为了满足该领域研究人员更高级的需求而设计的，另一个是为了高置信度比对的标准构建。基于网络的输出旨在通过五种默认颜色方案促进生成的比对的全面可视化，这些颜色方案基于：残基类型、位置保守性、位置可靠性、残基疏水性和二级结构，这取决于选项集。用户还可以通过选择哪种颜色将代表比对中的一个或多个氨基酸来定义自定义颜色方案。所有生成的路线也可在PDF格式，便于图形生成的出版物。比对所基于的序列分组也可以可视化为树状图。PRALINE可在。
PRofile ALIgNEment (PRALINE) is a fully customizable multiple sequence alignment application. In addition to a number of available alignment strategies, PRALINE can integrate information from database homology searches to generate a homology-extended multiple alignment. PRALINE also provides a choice of seven different secondary structure prediction programs that can be used individually or in combination as a consensus for integrating structural information into the alignment process. The program can be used through two separate interfaces: one has been designed to cater to more advanced needs of researchers in the field, and the other for standard construction of high confidence alignments. The web-based output is designed to facilitate the comprehensive visualization of the generated alignments by means of five default colour schemes based on: residue type, position conservation, position reliability, residue hydrophobicity and secondary structure, depending on the options set. A user can also define a custom colour scheme by selecting which colour will represent one or more amino acids in the alignment. All generated alignments are also made available in the PDF format for easy figure generation for publications. The grouping of sequences, on which the alignment is based, can also be visualized as a dendrogram. PRALINE is available at .