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An algorithm for searching RNA motifs in genomic sequences

Paper ID Volume ID Publish Year Pages File Format Full-Text
14158 1177 2007 8 PDF Available
Title
An algorithm for searching RNA motifs in genomic sequences
Abstract

RNA molecules, which are found in all living cells, fold into characteristic structures that account for their diverse functional activities. Many of these RNA structures consist of a collection of fundamental RNA motifs. The various combinations of RNA basic components form different RNA classes and define their unique structural and functional properties. The availability of many genome sequences makes it possible to search computationally for functional RNAs. Biological experiments indicate that functional RNAs have characteristic RNA structural motifs represented by specific combinations of base pairings and conserved nucleotides in the loop regions. The searching for those well-ordered RNA structures and their homologues in genomic sequences is very helpful for the understanding of RNA-based gene regulation. In this paper, we consider the following problem: given an RNA sequence with a known secondary structure, efficiently determine candidate segments in genomic sequences that can potentially form RNA secondary structures similar to the given RNA secondary structure. Our new bottom-up approach searches all potential stem-loops similar to ones of the given RNA secondary structure first, and then based on located stem-loops, detects potential homologous structural RNAs in genomic sequences.

Keywords
RNA stem-loop/stem; RNA tree representation; Pattern recognition; Homologous structural search
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An algorithm for searching RNA motifs in genomic sequences
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Publisher
Database: Elsevier - ScienceDirect
Journal: Biomolecular Engineering - Volume 24, Issue 3, September 2007, Pages 343–350
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us