iRMSD：一种利用结构信息衡量序列比对准确性的局部指标。
The iRMSD: a local measure of sequence alignment accuracy using structural information.
作者信息
Armougom Fabrice, Moretti Sébastien, Keduas Vladimir, Notredame Cedric
机构信息
Laboratoire Information Génomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM) Parc Scientifique de Luminy, case 934, 163 Avenue de Luminy, FR-13288, Marseille cedex 09.
出版信息
Bioinformatics. 2006 Jul 15;22(14):e35-9. doi: 10.1093/bioinformatics/btl218.
MOTIVATION
We introduce the iRMSD, a new type of RMSD, independent from any structure superposition and suitable for evaluating sequence alignments of proteins with known structures.
RESULTS
We demonstrate that the iRMSD is equivalent to the standard RMSD although much simpler to compute and we also show that it is suitable for comparing sequence alignments and benchmarking multiple sequence alignment methods. We tested the iRMSD score on 6 established multiple sequence alignment packages and found the results to be consistent with those obtained using an established reference alignment collection like Prefab.
AVAILABILITY
The iRMSD is part of the T-Coffee package and is distributed as an open source freeware (http://www.tcoffee.org/).
动机
我们引入了iRMSD，一种新型的均方根偏差（RMSD），它独立于任何结构叠加，适用于评估具有已知结构的蛋白质的序列比对。
结果
我们证明iRMSD与标准RMSD等效，尽管计算起来要简单得多，并且我们还表明它适用于比较序列比对和对多序列比对方法进行基准测试。我们在6个已建立的多序列比对程序包上测试了iRMSD分数，发现结果与使用像Prefab这样的已建立的参考比对集合所获得的结果一致。
可用性
iRMSD是T-Coffee程序包的一部分，并作为开源免费软件分发（http://www.tcoffee.org/）。
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