Title

Computational Tools For Rna Structural Motif Identification

Abstract

In general, the geometry-based RNA motif search tools are more specific, and the base-pairing pattern-based RNA motif search tools are more sensitive. Computationally, geometry-based tools usually use heuristics, while basepairing pattern-based tools can apply rigorous algorithms for the search. In terms of speed, the base-pairing pattern-based tools usually run faster because of their simplified modeling. It is difficult to conclude which method is preferable for RNA structural motif identification, since most of these computational tools cater for different RNA motif families. Users should first consider how their motif of interest is defined before choosing which tool to use. For instance, some motifs are defined by their most distinct geometric property (for example, kink-turn is characterised by its 'kink' and the turn between two helical regions, see Figure 1), while the others are defined by their base-pairing patterns (for example, the tandem sheared motif is defined by three consecutive sheared base-pairs). The size of the query motif should also be considered. When the motif of interest is fairly small (empirically, less than 6 nucleotides), the user may want to choose the more specific geometrybased tools to refine the results. On the other hand, if the query motif is large (more than 6 nucleotides), base-pairing pattern-based tools should also be tried to find more interesting hits.

Publication Date

11-1-2010

Publication Title

Bio Tech International

Volume

22

Issue

NOVEMBER

Number of Pages

6-9

Document Type

Article

Personal Identifier

scopus

Socpus ID

79953687415 (Scopus)

Source API URL

https://api.elsevier.com/content/abstract/scopus_id/79953687415

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