Universal sequence map (USM) of arbitrary discrete sequences.
Universal sequence map (USM) of arbitrary discrete sequences.
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DOI：
10.1186/1471-2105-3-6
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发表时间：
2002
影响因子：
3
通讯作者：
Vinga S
中科院分区：
文献类型：
--
作者：
Almeida JS;Vinga S
十多年来，在连续坐标空间中表示生物序列的想法一直保持着吸引力，但尚未完全实现。其基本思想是任何符号序列都可以在连续空间中定义轨迹，并保持其所有统计性质。理想情况下，这样的表示将允许规模无关的序列分析-没有固定内存长度的上下文。一个简单的例子是，仅仅通过比较任意两个同源单元的坐标就可以推断出两个序列之间的同源性。我们已经成功地识别了这样一个迭代函数，用于将离散序列的双射映射到连续状态空间的对象中，使序列分析与尺度无关。该技术被称为通用序列映射（USM），适用于具有任意长度和任意数量唯一单元的序列，并生成映射距离估计序列相似性的表示。新的USM程序是基于这些和其他作者关于混沌博弈表示（CGR）性质的早期工作。后者可以将4个单元型序列（如DNA）表示为无序马尔可夫链转移表。USM的特性是用测试数据说明的，可以通过使用附带的基于web的工具：http://bioinformatics.musc.edu/~jonas/usm/来验证其他数据。USM显示，使统计力学方法序列分析。尺度无关表示使序列分析在研究语法规则时不必假定一个记忆长度。
For over a decade the idea of representing biological sequences in a continuous coordinate space has maintained its appeal but not been fully realized. The basic idea is that any sequence of symbols may define trajectories in the continuous space conserving all its statistical properties. Ideally, such a representation would allow scale independent sequence analysis – without the context of fixed memory length. A simple example would consist on being able to infer the homology between two sequences solely by comparing the coordinates of any two homologous units. We have successfully identified such an iterative function for bijective mappingψ of discrete sequences into objects of continuous state space that enable scale-independent sequence analysis. The technique, named Universal Sequence Mapping (USM), is applicable to sequences with an arbitrary length and arbitrary number of unique units and generates a representation where map distance estimates sequence similarity. The novel USM procedure is based on earlier work by these and other authors on the properties of Chaos Game Representation (CGR). The latter enables the representation of 4 unit type sequences (like DNA) as an order free Markov Chain transition table. The properties of USM are illustrated with test data and can be verified for other data by using the accompanying web-based tool:http://bioinformatics.musc.edu/~jonas/usm/. USM is shown to enable a statistical mechanics approach to sequence analysis. The scale independent representation frees sequence analysis from the need to assume a memory length in the investigation of syntactic rules.
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影响因子：
3.1
作者：
Hill, KA;Singh, SM
通讯作者：
Singh, SM
影响因子：
3.5
作者：
MataToledo, RA;Willis, MA
通讯作者：
Willis, MA
影响因子：
2.9
作者：
Pleissner, KP;Wernisch, L;Fleck, E
通讯作者：
Fleck, E
DOI：
10.1007/s100960000321
发表时间：
2000-08-01
影响因子：
4.5
作者：
Enright, MC;Knox, K;Spratt, BG
通讯作者：
Spratt, BG
影响因子：
2.9
作者：
Basu, S;Pan, A;Das, J
通讯作者：
Das, J