Journal Article

AQUA: automated quality improvement for multiple sequence alignments

Jean Muller, Christopher J. Creevey, Julie D. Thompson, Detlev Arendt and Peer Bork

in Bioinformatics

Volume 26, issue 2, pages 263-265
Published in print January 2010 | ISSN: 1367-4803
Published online November 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp651
AQUA: automated quality improvement for multiple sequence alignments

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Summary: Multiple sequence alignment (MSA) is a central tool in most modern biology studies. However, despite generations of valuable tools, human experts are still able to improve automatically generated MSAs. In an effort to automatically identify the most reliable MSA for a given protein family, we propose a very simple protocol, named AQUA for ‘Automated quality improvement for multiple sequence alignments’. Our current implementation relies on two alignment programs (MUSCLE and MAFFT), one refinement program (RASCAL) and one assessment program (NORMD), but other programs could be incorporated at any of the three steps.

Availability: AQUA is implemented in Tcl/Tk and runs in command line on all platforms. The source code is available under the GNU GPL license. Source code, README and Supplementary data are available at http://www.bork.embl.de/Docu/AQUA.

Contact: muller@embl.de, bork@embl.de

Journal Article.  1350 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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