A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements

29Citations
Citations of this article
58Readers
Mendeley users who have this article in their library.

This article is free to access.

Abstract

Motivation: Recent studies have uncovered an "RNA world", in which non coding RNA (ncRNA) sequences play a central role in the regulation of gene expression. Computational studies on ncRNA have been directed toward developing detection methods for ncRNAs. State-of-the-art methods for the problem, like covariance models, suffer from high computational cost, underscoring the need for efficient filtering approaches that can identify promising sequence segments and speedup the detection process. Results: In this paper we make several contributions toward this goal. First, we formalize the concept of a filter and provide figures of merit that allow comparison between filters. Second, we design efficient sequence based filters that dominate the current state-of-the-art HMM filters. Third, we provide a new formulation of the covariance model that allows speeding up RNA alignment. We demonstrate the power of our approach on both synthetic data and real bacterial genomes. We then apply our algorithm to the detection of novel riboswitch elements from the whole bacterial and archaeal genomes. Our results point to a number of novel riboswitch candidates, and include genomes that were not previously known to contain riboswitches. © 2006 Oxford University Press.

References Powered by Scopus

Rfam: Annotating non-coding RNAs in complete genomes

1306Citations
N/AReaders
Get full text

Rfam: An RNA family database

1257Citations
N/AReaders
Get full text

Non-coding RNA genes and the modern RNA world

1122Citations
N/AReaders
Get full text

Cited by Powered by Scopus

Hidden Markov models and their applications in biological sequence analysis

258Citations
N/AReaders
Get full text

Query-dependent banding (QDB) for faster RNA similarity searches

255Citations
N/AReaders
Get full text

RNAMotifScan: Automatic identification of RNA structural motifs using secondary structural alignment

41Citations
N/AReaders
Get full text

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Cite

CITATION STYLE

APA

Zhang, S., Borovok, I., Aharonowitz, Y., Sharan, R., & Bafna, V. (2006). A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements. In Bioinformatics (Vol. 22). Oxford University Press. https://doi.org/10.1093/bioinformatics/btl232

Readers over time

‘09‘10‘11‘12‘13‘14‘15‘16‘17‘18‘19‘20‘21‘22‘23‘24036912

Readers' Seniority

Tooltip

PhD / Post grad / Masters / Doc 25

51%

Researcher 16

33%

Professor / Associate Prof. 8

16%

Readers' Discipline

Tooltip

Agricultural and Biological Sciences 24

50%

Biochemistry, Genetics and Molecular Bi... 12

25%

Computer Science 11

23%

Design 1

2%

Save time finding and organizing research with Mendeley

Sign up for free
0