Böcker Sebastian, Wagner Stephan
Lehrstuhl für Bioinformatik, Friedrich-Schiller-Universität Jena, Ernst-Abbe-Platz 2, Jena, Germany,
J Math Biol. 2014 Oct;69(4):799-816. doi: 10.1007/s00285-013-0721-3. Epub 2013 Aug 23.
We present an algorithm for counting glycan topologies of order n that improves on previously described algorithms by a factor n in both time and space. More generally, we provide such an algorithm for counting rooted or unrooted d-ary trees with labels or masses assigned to the vertices, and we give a "recipe" to estimate the asymptotic growth of the resulting sequences. We provide constants for the asymptotic growth of d-ary trees and labeled quaternary trees (glycan topologies). Finally, we show how a classical result from enumeration theory can be used to count glycan structures where edges are labeled by bond types. Our method also improves time bounds for counting alkanes.
我们提出了一种用于计算n阶聚糖拓扑结构的算法,该算法在时间和空间上比先前描述的算法都有n倍的提升。更一般地,我们提供了这样一种算法,用于计算顶点被赋予标签或质量的有根或无根d叉树,并且我们给出了一个“方法”来估计所得序列的渐近增长。我们给出了d叉树和带标签的四叉树(聚糖拓扑结构)渐近增长的常数。最后,我们展示了如何使用枚举理论中的一个经典结果来计算边由键类型标记的聚糖结构。我们的方法还改进了计算烷烃的时间界限。