Gorodkin J, Heyer L J, Brunak S, Stormo G D
Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark.
Comput Appl Biosci. 1997 Dec;13(6):583-6. doi: 10.1093/bioinformatics/13.6.583.
We extend the standard 'Sequence Logo' method of Schneider and Stevens (Nucleic Acids Res., 18, 6097-6100, 1990) to incorporate prior frequencies on the bases, allow for gaps in the alignments, and indicate the mutual information of base-paired regions in RNA.
Given an alignment of RNA sequences with the base pairings indicated, the program will calculate the information at each position, including the mutual information of the base pairs, and display the results in a 'Structure Logo'. Alignments without base pairing can also be displayed in a 'Sequence Logo', but still allowing gaps and incorporating prior frequencies if desired.
The code is available from, and an Internet server can be used to run the program at, http://www.cbs.dtu.dk/gorodkin/appl/slogo. html.
我们扩展了施奈德和史蒂文斯（《核酸研究》，第18卷，6097 - 6100页，1990年）的标准“序列标识”方法，以纳入碱基的先验频率，允许比对中存在空位，并显示RNA中碱基配对区域的互信息。
给定一个带有碱基配对指示的RNA序列比对，该程序将计算每个位置的信息，包括碱基对的互信息，并以“结构标识”显示结果。没有碱基配对的比对也可以以“序列标识”显示，但仍允许有空位，并可根据需要纳入先验频率。
代码可从http://www.cbs.dtu.dk/gorodkin/appl/slogo.html获取，也可以使用互联网服务器在该网站运行该程序。
