AQUA: automated quality improvement for multiple sequence alignments

Bioinformatics
Jean MullerPeer Bork

Abstract

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. 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.

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Citations

Oct 22, 2013·Nature Methods·Shinichi SunagawaPeer Bork
Mar 16, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·John Kececioglu, Dan DeBlasio
Nov 20, 2012·Genome Biology and Evolution·David WilliamsR Thane Papke
Jun 10, 2010·Nucleic Acids Research·Mohamed Radhouene AnibaJulie Dawn Thompson
Nov 19, 2013·BMC Evolutionary Biology·Claire C MorganMary J O'Connell
Sep 24, 2010·PLoS Computational Biology·Thomas S RaskThomas Lavstsen
Dec 7, 2011·PLoS Computational Biology·Christopher J CreeveyPeer Bork
Nov 12, 2013·Applied and Environmental Microbiology·Ciara A CarberryChristopher J Creevey
Feb 19, 2016·Glycobiology·Alexey A Morozov, Yelena V Likhoshway
Sep 3, 2011·Environmental Microbiology·Nof Atamna-IsmaeelShimshon Belkin
Jul 19, 2012·Molecular Systems Biology·Pablo MinguezPeer Bork
Sep 10, 2010·Clinical Genetics·Melanie FradinB Doray
May 6, 2015·Proceedings of the National Academy of Sciences of the United States of America·Aleksej ZelezniakKiran Raosaheb Patil
Mar 27, 2013·Journal of Biomolecular Structure & Dynamics·Aparna RoySree V Chintapalli
Jul 31, 2013·Nature Methods·Daniel R MendePeer Bork
Jul 14, 2018·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Jordi LladósFernando Guirado
Mar 25, 2019·Molecular Biology and Evolution·Karen Siu-TingChristopher J Creevey
Aug 20, 2011·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Kalliopi TrachanaPeer Bork
Feb 15, 2018·Science Advances·Nicole M FoleyEmma C Teeling
Jun 6, 2018·International Journal of Environmental Health Research·Sabaridasan Arumugam, Soranam Ramaiah
Oct 2, 2020·PLoS Neglected Tropical Diseases·Pasi K KorhonenKatja Fischer
Mar 27, 2019·Molecular Biology and Evolution·Reetu TutejaCharles Spillane
Oct 27, 2018·International Journal of Molecular Sciences·Cindy P Ulloa-GuerreroCarlos A Jaramillo
Oct 7, 2020·Genome Biology and Evolution·David M Emms, Steven Kelly

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