Automatic generation of primary sequence patterns from sets of related protein sequences.
Automatic generation of primary sequence patterns from sets of related protein sequences.
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DOI：
10.1073/pnas.87.1.118
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发表时间：
1990
影响因子：
11.1
通讯作者：
Randall F. Smith;Temple F. Smith
中科院分区：
文献类型：
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作者：
Randall F. Smith;Temple F. Smith
我们已经开发了一种计算机算法，可以提取的模式保守的一级序列元素共同的同源蛋白质家族的所有成员。该方法涉及在一组相关序列之间聚类成对相似性得分以生成二元树状图（树）。然后，通过用一个共同的模式逐步替换连接两个最相似的端点的节点，直到只剩下一个共同的“根”模式，以逐步的方式减少树。通过以下步骤在节点处生成模式：（i）使用扩展的动态编程算法对由节点连接的序列/模式对进行局部最优比对，然后（ii）从该比对与氨基酸类的嵌套层次结构构建单个共同模式，以鉴定覆盖比对中的每个成对元素集的最小包含性氨基酸类。使用“一次支付”空位罚分规则创建和/或延伸比对内的空位，并且将空位位置转换成在后续比对期间充当任何类型的0或1个氨基酸的空位字符。该方法已被用来产生一个库的覆盖模式的同源家庭在国家生物医学研究基金会/蛋白质鉴定资源蛋白质序列数据库。我们发现，覆盖模式可以更诊断序列家族成员比任何用于构建模式的单个序列。
We have developed a computer algorithm that can extract the pattern of conserved primary sequence elements common to all members of a homologous protein family. The method involves clustering the pairwise similarity scores among a set of related sequences to generate a binary dendrogram (tree). The tree is then reduced in a stepwise manner by progressively replacing the node connecting the two most similar termini by one common pattern until only a single common "root" pattern remains. A pattern is generated at a node by (i) performing a local optimal alignment on the sequence/pattern pair connected by the node with the use of an extended dynamic programming algorithm and then (ii) constructing a single common pattern from this alignment with a nested hierarchy of amino acid classes to identify the minimal inclusive amino acid class covering each paired set of elements in the alignment. Gaps within an alignment are created and/or extended using a "pay once" gap penalty rule, and gapped positions are converted into gap characters that function as 0 or 1 amino acid of any type during subsequent alignment. This method has been used to generate a library of covering patterns for homologous families in the National Biomedical Research Foundation/Protein Identification Resource protein sequence data base. We show that a covering pattern can be more diagnostic for sequence family membership than any of the individual sequences used to construct the pattern.