MIp工具集：一种计算蛋白质比对互信息的高效算法
The MIp Toolset: an efficient algorithm for calculating Mutual Information in protein alignments
摘要：
背景资料：蛋白质家族内的共同进化通常是通过统计学来预测的，这些统计学测量了蛋白质序列中位置之间的共同变异程度。互信息是两个随机变量之间依赖性的度量，已被广泛用于预测蛋白质内的协同进化。结果：在这里，我们提供了一个算法的有效计算的蛋白质家族内的互信息。该算法使用的链表是直接访问的指针数组。链表允许有效存储由蛋白质保守引起的稀疏计数数据。指针的直接访问数组防止每次修改链表时遍历链表。结论：该算法在软件MIpToolset中实现，但也可以在其他基于互信息的独立软件或Web服务器中轻松实现。MIpToolset中的当前实现在比对编辑和策展期间的大规模蛋白质家族分析和实时协同进化计算中至关重要。MIpToolset可从以下网址获得：https://sourceforge.net/projects/miptoolset/
英文摘要：
Background: Coevolution within a protein family is often predicted using statistics that measure the degree of covariation between positions in the protein sequence. Mutual Information is a measure of dependence between two random variables that has been used extensively to predict intra-protein coevolution. Results: Here we provide an algorithm for the efficient calculation of Mutual Information within a protein family. The algorithm uses linked lists which are directly accessed by a pointer array. The linked list allows efficient storage of sparse count data caused by protein conservation. The direct access array of pointers prevents the linked list from being traversed each time it is modified. Conclusions: This algorithm is implemented in the software MIpToolset, but could also be easily implemented in other Mutual Information based standalone software or web servers. The current implementation in the MIpToolset has been critical in large-scale protein family analysis and real-time coevolution calculations during alignment editing and curation. The MIpToolset is available at: https://sourceforge.net/projects/miptoolset/
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