Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE.

BMC research notes ·Vol. 1 ·2008-10-14 ·Pages 91

Seibel PN, Müller T, Dandekar T, Wolf M

Abstract

The function of a noncoding RNA sequence is mainly determined by its secondary structure and therefore a family of noncoding RNA sequences is much more conserved on the structural level than on the sequence level. Understanding the function of noncoding RNA sequence families requires two things: a hand-crafted or hand-improved alignment and detailed analyses of the secondary structures. There are several tools available that help performing these tasks, but all of them are specialized and focus on only one aspect, editing the alignment or plotting the secondary structure. The problem is both these tasks need to be performed simultaneously. 4SALE is designed to handle sequence and secondary structure information of RNAs synchronously. By including a complete new method of simultaneous visualization and editing RNA sequences and secondary structure information, 4SALE enables to improve and understand RNA sequence and secondary structure evolution much more easily. 4SALE is a step further for simultaneously handling RNA sequence and secondary structure information. It provides a complete new way of visual monitoring different structural aspects, while editing the alignment. The software is freely available and distributed from its website at http://4sale.bioapps.biozentrum.uni-wuerzburg.de/

Authors & Affiliations

4 authors, click to expand affiliations / ORCID

Seibel Philipp N

Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany. philipp.seibel@biozentrum.uni-wuerzburg.de

Müller Tobias

Dandekar Thomas

Wolf Matthias

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Article Info

Journal

BMC research notes

Abbr.

BMC Res Notes

ISSN

1756-0500

DOI

10.1186/1756-0500-1-91

philipp.seibel@biozentrum.uni-wuerzburg.de

Published

2008-10-14

Epub

2008-00-14

Pages

Language

English

Region

England

NLM ID

101462768

PMCID

PMC2587473

External Links

PubMed source DOI: 10.1186/1756-0500-1-91 PMC Full Text View journal details

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Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE.

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