Amino acid substitution matrices from an information theoretic perspective.
Amino acid substitution matrices from an information theoretic perspective.
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DOI：
10.1016/0022-2836(91)90193-a
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发表时间：
1991-06-05
影响因子：
5.6
通讯作者：
Altschul SF
中科院分区：
文献类型：
--
作者：
Altschul SF
蛋白质序列比对已成为分子生物学家的重要工具。局部比对通常是借助于“替代分数矩阵”来构建的，该矩阵指定了对每对氨基酸残基进行比对的分数。多年来，基于各种各样的原理，提出了许多不同的替代矩阵。然而，统计结果表明，任何这样的矩阵都是隐含的“对数概率”矩阵，对氨基酸残基对具有特定的目标分布。根据信息论，可以用比特来表示替换矩阵的分数，并且可以看出不同的矩阵更适合于不同的目的。最广泛用于蛋白质序列比较的基质是PAM-250基质。对于数据库搜索，PAM-120矩阵通常更合适，而对于两个具有疑似同源性的特定蛋白质的比较，PAM-200矩阵则更合适。讨论的例子包括脂载蛋白、人α 1b糖蛋白、囊性纤维化跨膜传导调节剂和珠蛋白。
Protein sequence alignments have become an important tool for molecular biologists. Local alignments are frequently constructed with the aid of a “substitution score matrix” that specifies a score for aligning each pair of amino acid residues. Over the years, many different substitution matrices have been proposed, based on a wide variety of rationales. Statistical results, however, demonstrate that any such matrix is implicitly a “log-odds” matrix, with a specific target distribution for aligned pairs of amino acid residues. In the light of information theory, it is possible to express the scores of a substitution matrix in bits and to see that different matrices are better adapted to different purposes. The most widely used matrix for protein sequence comparison has been the PAM-250 matrix. It is argued that for database searches the PAM-120 matrix generally is more appropriate, while for comparing two specific proteins with suspected homology the PAM-200 matrix is indicated. Examples discussed include the lipocalins, human α1B-glycoprotein, the cystic fibrosis transmembrane conductance regulator and the globins.
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影响因子：
3.5
作者：
ALTSCHUL, SF;ERICKSON, BW
通讯作者：
ERICKSON, BW
影响因子：
1
作者：
ARRATIA, R;MORRIS, P;WATERMAN, MS
通讯作者：
WATERMAN, MS
DOI：
10.1089/dna.1987.6.199
发表时间：
1987-06-01
期刊：
DNA-A JOURNAL OF MOLECULAR & CELLULAR BIOLOGY
影响因子：
--
作者：
DRAYNA, DT;MCLEAN, JW;LAWN, RM
通讯作者：
LAWN, RM
影响因子：
3.9
作者：
FENG, DF;JOHNSON, MS;DOOLITTLE, RF
通讯作者：
DOOLITTLE, RF
影响因子：
64.8
作者：
HIGGINS, CF;HILES, ID;HERMODSON, MA
通讯作者：
HERMODSON, MA