Grammar-based compression approach to extraction of common rules among multiple trees of glycans and RNAs.
BMC Bioinformatics
; 16: 128, 2015 Apr 24.
Article
em En
| MEDLINE
| ID: mdl-25907438
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 systems, and can be regarded as tree structures. The results suggest that our method can be successfully applied to determining the minimum grammar and several common rules among glycans and RNAs. CONCLUSIONS: We propose integer programming-based methods MinSEOTGMul and MinSEUTGMul for the determination of the minimum grammars constructing multiple ordered and unordered trees, respectively. The proposed methods can provide clues for the determination of hierarchical structures contained in tree-structured biological data, beyond the extraction of frequent patterns.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Polissacarídeos
/
Algoritmos
/
RNA
/
Compressão de Dados
Limite:
Humans
Idioma:
En
Revista:
BMC Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2015
Tipo de documento:
Article
País de afiliação:
Japão
País de publicação:
Reino Unido