A New Structure Representation for RNA and Fast RNA Substructure Search

A New Structure Representation for RNA and Fast RNA Substructure Search

We propose a new representation for RNA structures. The new representation has important features by which we create and store an RNA database into a suffix array. We present a search algorithm that finds all matches to a given substructure in the database. Our tests show that this method is signifi...

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Bibliographic Details
Published in:2016 International Conference on Computational Science and Computational Intelligence (CSCI) pp. 1226 - 1231
Main Authors: Arslan, Abdullah N., Anandan, Jithendar, Fry, Eric, Pandey, Rabindra, Monschke, Keith
Format: Conference Proceeding
Language:English
Published: IEEE 01-12-2016
Subjects:
Arrays
Context
Grammar
Indexes
RNA
RNA substructure representation
search
suffix array
Two dimensional displays
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Description
Summary:We propose a new representation for RNA structures. The new representation has important features by which we create and store an RNA database into a suffix array. We present a search algorithm that finds all matches to a given substructure in the database. Our tests show that this method is significantly faster than other existing search methods. We launch a website with the substructure search tool.
DOI:10.1109/CSCI.2016.0231