SICOR: Subgraph Isomorphism Comparison of RNA Secondary Structures

Michael Schmidt; Kay Hamacher; Felix Reinhardt; Thea S Lotz; Florian Groher; Beatrix Suess; Sven Jager

doi:10.1109/TCBB.2019.2926711

SICOR: Subgraph Isomorphism Comparison of RNA Secondary Structures

IEEE/ACM Trans Comput Biol Bioinform. 2020 Nov-Dec;17(6):2189-2195. doi: 10.1109/TCBB.2019.2926711. Epub 2020 Dec 8.

Authors

Michael Schmidt, Kay Hamacher, Felix Reinhardt, Thea S Lotz, Florian Groher, Beatrix Suess, Sven Jager

PMID: 31295116
DOI: 10.1109/TCBB.2019.2926711

Abstract

RNA aptamer selection during SELEX experiments builds on secondary structural diversity. Advanced structural comparison methods can focus this diversity. We develop SICOR, which uses probabilistic subgraph isomorphisms for graph distances between RNA secondary structure graphs. SICOR outperforms other comparison methods and is applicable to many structural comparisons in experimental design.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Aptamers, Nucleotide / chemistry*
Computational Biology / methods*
Databases, Nucleic Acid
Databases, Pharmaceutical
Nucleic Acid Conformation
RNA / chemistry*
SELEX Aptamer Technique / methods*

Substances

Aptamers, Nucleotide
RNA