COACH:: profile-profile alignment of protein families using hidden Markov models
COACH:: profile-profile alignment of protein families using hidden Markov models
复制标题
DOI：
10.1093/bioinformatics/bth091
复制
发表时间：
2004-05-22
期刊：
影响因子：
5.8
通讯作者：
Sjölander, K
中科院分区：
文献类型：
--
作者：
Edgar, RC;Sjölander, K
动机：两个多序列比对的比对，或这种比对的统计模型(Profile)，在计算生物学中有重要的应用。与单一序列相比，图谱中信息量的增加可以导致数据库搜索中更准确的比对和更灵敏的同源检测。已经提出了几种轮廓-轮廓比对方法，并且已经被证明与序列-序列方法(例如BLAST)和轮廓-序列方法(例如PSI-BLAST)相比可以提高灵敏度和比对质量。在这里，我们提出了一种新的轮廓-轮廓比对方法，我们称之为通过构建隐马尔可夫模型(HMM)(COACH)进行比对。Coach通过根据一个比对构造一个Profile HMM并将另一个比对到该HMM来比对两个多序列比对。结果：我们将Coach的比对精度与最近发表的两种方法进行了比较：Yona和Levitt的prof_sim和Sadreyev和Grishin的指南针。在从FSSP数据库中选择的两组参考路线上，我们发现Coach平均能够产生给出最佳覆盖或最小误差的路线，这取决于所选择的参数设置。
Motivation: Alignments of two multiple-sequence alignments, or statistical models of such alignments (profiles), have important applications in computational biology. The increased amount of information in a profile versus a single sequence can lead to more accurate alignments and more sensitive homolog detection in database searches. Several profile-profile alignment methods have been proposed and have been shown to improve sensitivity and alignment quality compared with sequence-sequence methods (such as BLAST) and profile-sequence methods (e.g. PSI-BLAST). Here we present a new approach to profile-profile alignment we call Comparison of Alignments by Constructing Hidden Markov Models (HMMs) (COACH). COACH aligns two multiple sequence alignments by constructing a profile HMM from one alignment and aligning the other to that HMM.Results: We compare the alignment accuracy of COACH with two recently published methods: Yona and Levitt's prof_sim and Sadreyev and Grishin's COMPASS. On two sets of reference alignments selected from the FSSP database, we find that COACH is able, on average, to produce alignments giving the best coverage or the fewest errors, depending on the chosen parameter settings.