CLUSTAL-W - IMPROVING THE SENSITIVITY OF PROGRESSIVE MULTIPLE SEQUENCE ALIGNMENT THROUGH SEQUENCE WEIGHTING, POSITION-SPECIFIC GAP PENALTIES AND WEIGHT MATRIX CHOICE
CLUSTAL-W - IMPROVING THE SENSITIVITY OF PROGRESSIVE MULTIPLE SEQUENCE ALIGNMENT THROUGH SEQUENCE WEIGHTING, POSITION-SPECIFIC GAP PENALTIES AND WEIGHT MATRIX CHOICE
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DOI：
10.1093/nar/22.22.4673
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发表时间：
1994-11-11
影响因子：
14.9
通讯作者：
GIBSON, TJ
中科院分区：
文献类型：
--
作者：
THOMPSON, JD;HIGGINS, DG;GIBSON, TJ
为了提高渐进式多序列比对方法在不同蛋白质序列比对中的灵敏度，首先对部分比对中的每个序列赋予单独的权值，以降低相似序列的权值，提高差异最大序列的权值。其次，根据待比对序列的差异，在不同的比对阶段改变氨基酸取代矩阵。第三，残基特异性空位罚分和亲水区域中局部减少的空位罚分鼓励潜在环区域中的新空位而不是常规二级结构。第四，在早期比对中，空位已经打开的位置接收局部减少的空位罚分，以鼓励在这些位置打开新的空位。这些修改被纳入一个新的程序，CLUSTAL W，这是免费提供的。
The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences, Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gap at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.