Suffix Techniques as a Rapid Method for Rna Substructure Search

Bauer, Raphael André; Rother, Kristian; Bujnicki, Janusz M.; Preißner, Robert

doi:10.1142/9781848163003_0016

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“…The proposed approach performs a search for local structural motifs in a set of 3D structures of macromolecules. The basic ideas for this approach originate in [36], where we analyzed different possibilities to represent RNA structures as a reduced alphabet and the possibility of storing and querying that alphabet in suffix-based indices. The paper clearly shows that the proposed methodology of suite codes [32] is too narrow for a RNA search.…”

Section: In a Nutshellmentioning

confidence: 99%

Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors

et al. 2009

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This work presents a generalized approach for the fast structural alignment of thousands of macromolecular structures. The method uses string representations of a macromolecular structure and a hash table that stores n-grams of a certain size for searching. To this end, macromolecular structure-to-string translators were implemented for protein and RNA structures. A query against the index is performed in two hierarchical steps to unite speed and precision. In the first step the query structure is translated into n-grams, and all target structures containing these n-grams are retrieved from the hash table. In the second step all corresponding n-grams of the query and each target structure are subsequently aligned, and after each alignment a score is calculated based on the matching n-grams of query and target. The extendable framework enables the user to query and structurally align thousands of protein and RNA structures on a commodity machine and is available as open source from http://lajolla.sf.net

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Section: In a Nutshellmentioning

confidence: 99%