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RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

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An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery

Akito Taneda1

  • 1Graduate School of Science and Technology, Hirosaki University, Hirosaki, Japan. taneda@eit.hirosaki-u.ac.jp

BMC Bioinformatics
|December 9, 2008
PubMed
Summary

A new genetic algorithm, Cofolga2, efficiently aligns RNA sequences and predicts novel non-coding RNA (ncRNA) candidates. This tool aids large-scale ncRNA discovery by considering structural conservation in low-sequence-identity alignments.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • RNA sequence alignment with low sequence identity is computationally challenging due to the need for structural conservation.
  • Existing algorithms require efficiency improvements for large-scale applications like non-coding RNA (ncRNA) discovery.

Purpose of the Study:

  • To develop an efficient algorithm for simultaneous RNA sequence alignment and consensus folding.
  • To apply the developed algorithm for novel ncRNA discovery.

Main Methods:

  • Developed Cofolga2, a novel genetic algorithm for pairwise RNA sequence alignment and consensus folding.
  • Benchmarked Cofolga2 using BRAliBase 2.1 for accuracy and efficiency.
  • Applied Cofolga2 combined with a Support Vector Machine (SVM) to compare S. cerevisiae with six related genomes for ncRNA discovery.

Main Results:

  • Cofolga2 demonstrated accuracy and efficiency in time and memory usage.
  • Successfully predicted 714 intergenic and 1,311 sense/antisense ncRNA candidates with stable secondary structures and low sequence identity (
  • Over 92% of predicted candidates were novel; 25% of intergenic candidates showed evidence of expression.

Conclusions:

  • Cofolga2 provides an efficient computational tool for RNA sequence analysis.
  • The method complements existing sequence-alignment-based ncRNA discovery tools.