Grammar-based compression approach to extraction of common rules among multiple trees of glycans and RNAs.

ABSTRACT:

Background

Many tree structures are found in nature and organisms. Such trees are believed to be constructed on the basis of certain rules. We have previously developed grammar-based compression methods for ordered and unordered single trees, based on bisection-type tree grammars. Here, these methods find construction rules for one single tree. On the other hand, specified construction rules can be utilized to generate multiple similar trees.

Results

Therefore, in this paper, we develop novel methods to discover common rules for the construction of multiple distinct trees, by improving and extending the previous methods using integer programming. We apply our proposed methods to several sets of glycans and RNA secondary structures, which play important roles in cellular syst

SUBMITTER: Zhao Y 

PROVIDER: S-EPMC4419412 | biostudies-literature | 2015 Apr

REPOSITORIES: biostudies-literature