Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues.
Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues.
复制标题
DOI：
10.1093/nar/gkn945
复制
发表时间：
2009-02
影响因子：
14.9
通讯作者：
Sze, Sing-Hoi
中科院分区：
文献类型：
--
作者：
Lu, Yue;Sze, Sing-Hoi
虽然最近在多序列比对准确性方面的大部分改进是由于更好地使用垂直信息，包括结合基于一致性的成对比对和使用轮廓比对，但我们观察到，当比对两个残基时，通过考虑相邻残基的比对，可以进一步提高准确性，从而更好地利用水平信息。通过修改现有的多比对算法，利用水平信息，我们表明，这种策略是能够一贯地提高现有的算法上的几组基准比对，通常用于衡量比对精度，和平均精度的提高可以高达1-3%的蛋白质序列比对和5-10%的DNA/RNA序列比对。与以前的算法不同，可以在所有身份级别上获得一致的平均改进。
While most of the recent improvements in multiple sequence alignment accuracy are due to better use of vertical information, which include the incorporation of consistency-based pairwise alignments and the use of profile alignments, we observe that it is possible to further improve accuracy by taking into account alignment of neighboring residues when aligning two residues, thus making better use of horizontal information. By modifying existing multiple alignment algorithms to make use of horizontal information, we show that this strategy is able to consistently improve over existing algorithms on a few sets of benchmark alignments that are commonly used to measure alignment accuracy, and the average improvements in accuracy can be as much as 1–3% on protein sequence alignment and 5–10% on DNA/RNA sequence alignment. Unlike previous algorithms, consistent average improvements can be obtained across all identity levels.
登录
查看更多内容
DOI：
10.1073/pnas.89.22.10915
发表时间：
1992-11-15
影响因子：
11.1
作者：
HENIKOFF, S;HENIKOFF, JG
通讯作者：
HENIKOFF, JG
影响因子：
14.9
作者：
Griffiths-Jones, S;Bateman, A;Eddy, SR
通讯作者：
Eddy, SR
影响因子：
1.1
作者：
HUANG, XQ;MILLER, W
通讯作者：
MILLER, W
影响因子：
5.8
作者：
Capra, John A.;Singh, Mona
通讯作者：
Singh, Mona
影响因子：
8
作者：
Marti-Renom, MA;Madhusudhan, MS;Sali, A
通讯作者：
Sali, A