COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance
COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance
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DOI：
10.1016/s0022-2836(02)01371-2
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发表时间：
2003-02-07
影响因子：
5.6
通讯作者：
Grishin, N
中科院分区：
文献类型：
--
作者：
Sadreyev, R;Grishin, N
我们提出了一种通过统计显着性评估来比较多个蛋白质比对的新方法（COMPASS）。该方法从比对中得出数值轮廓，构建最佳的局部轮廓-轮廓比对，并分析估计检测到的相似性的 E 值。评分系统和 E 值计算基于 PSI-BLAST 方法对轮廓-序列比较的概括，该方法适用于轮廓-轮廓情况。与现有的轮廓-序列 (PSI-BLAST) 和轮廓-轮廓 (prof_sim) 比较方法一起进行测试，COMPASS 显示出增强的灵敏和选择性检测远程序列相似性的能力，以及提高的局部比对质量。该方法可以预测 PFAM 数据库中蛋白质家族之间的关系，超出了传统方法的范围。两个具有高度显着性的预测关系是各种罗斯曼型折叠之间以及各种包含螺旋-转角-螺旋家族之间的相似性。通过检测 CTF/NFI 家族的 DNA 结合结构域和 Smad 家族的 MH1 结构域之间复杂的同源性，说明了 COMPASS 在结构/功能预测方面的潜在价值。 (C) 2003 Elsevier Science Ltd. 保留所有权利。
We present a novel method for the comparison of multiple protein alignments with assessment of statistical significance (COMPASS). The method derives numerical profiles from alignments, constructs optimal local profile-profile alignments and analytically estimates E-values for the detected similarities. The scoring system and E-value calculation are based on a generalization of the PSI-BLAST approach to profile-sequence comparison, which is adapted for the profile-profile case. Tested along with existing methods for profile-sequence (PSI-BLAST) and profile-profile (prof_sim) comparison, COMPASS shows increased abilities for sensitive and selective detection of remote sequence similarities, as well as improved quality of local alignments. The method allows prediction of relationships between protein families in the PFAM database beyond the range of conventional methods. Two predicted relations with high significance are similarities between various Rossmann-type folds and between various helix-turn-helix-containing families. The potential value of COMPASS for structure/function predictions is illustrated by the detection of an intricate homology between the DNA-binding domain of the CTF/NFI family and the MH1 domain of the Smad family. (C) 2003 Elsevier Science Ltd. All rights reserved.