Application of a new probabilistic model for recognizing complex patterns in glycans
Application of a new probabilistic model for recognizing complex patterns in glycans
复制标题
DOI：
10.1093/bioinformatics/bth916
复制
发表时间：
2004-08-04
期刊：
影响因子：
5.8
通讯作者：
Mamitsuka, Hiroshi
中科院分区：
文献类型：
--
作者：
Aoki, Kiyoko F.;Ueda, Nobuhisa;Mamitsuka, Hiroshi
动机：碳水化合物糖链或聚糖的研究进展缓慢，主要是由于难以建立分析其结构和生物合成的标准方法。聚糖通常是比线性DNA或蛋白质序列更复杂的树状结构，并且有证据表明，聚糖中的模式可能存在于兄弟姐妹之间并进入不受实际树状结构本身中的边缘限制的进一步区域。目前的模型是不能够捕捉到这样的patterns.Results：我们已经应用了一种新的概率模型，称为概率兄弟依赖树马尔可夫模型（PSTMM），这是能够固有地捕捉这种复杂的模式的聚糖。不仅捕获这种模式的能力本身很重要，而且这也意味着PSTMM能够有效地执行多个树结构比对。我们通过对实际聚糖数据的实验证明，这种新模型对于深入了解聚糖的隐藏，复杂模式非常有用，这对更高层次生物的发展和功能至关重要。此外，我们还表明，该模型可以额外利用作为一种创新的方法，多树对齐，这还没有被应用到聚糖链之前。PSTMM使用的这种扩展可能不仅是聚糖结构分析的重要一步，而且可能因此证明有助于发现其功能的线索。
Motivation: The study of carbohydrate sugar chains, or glycans, has been one of slow progress mainly due to the difficulty in establishing standard methods for analyzing their structures and biosynthesis. Glycans are generally tree structures that are more complex than linear DNA or protein sequences, and evidence shows that patterns in glycans may be present that spread across siblings and into further regions that are not limited by the edges in the actual tree structure itself. Current models were not able to capture such patterns.Results: We have applied a new probabilistic model, called probabilistic sibling-dependent tree Markov model (PSTMM), which is able to inherently capture such complex patterns of glycans. Not only is the ability to capture such patterns important in itself, but this also implies that PSTMM is capable of performing multiple tree structure alignments efficiently. We prove through experimentation on actual glycan data that this new model is extremely useful for gaining insight into the hidden, complex patterns of glycans, which are so crucial for the development and functioning of higher level organisms. Furthermore, we also show that this model can be additionally utilized as an innovative approach to multiple tree alignment, which has not been applied to glycan chains before. This extension on the usage of PSTMM may be a major step forward for not only the structural analysis of glycans, but it may consequently prove useful for discovering clues into their function.