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Bioinformatics Advance Access originally published online on July 30, 2009
Bioinformatics 2009 25(19):2455-2465; doi:10.1093/bioinformatics/btp452
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Upcoming challenges for multiple sequence alignment methods in the high-throughput era

Carsten Kemena and Cedric Notredame *

Centre For Genomic Regulation (Pompeus Fabre University), Carrer del Doctor Aiguader 88, 08003 Barcelona, Spain

* To whom correspondence should be addressed.


  Abstract

This review focuses on recent trends in multiple sequence alignment tools. It describes the latest algorithmic improvements including the extension of consistency-based methods to the problem of template-based multiple sequence alignments. Some results are presented suggesting that template-based methods are significantly more accurate than simpler alternative methods. The validation of existing methods is also discussed at length with the detailed description of recent results and some suggestions for future validation strategies. The last part of the review addresses future challenges for multiple sequence alignment methods in the genomic era, most notably the need to cope with very large sequences, the need to integrate large amounts of experimental data, the need to accurately align non-coding and non-transcribed sequences and finally, the need to integrate many alternative methods and approaches.

Contact: cedric.notredame{at}crg.es

Associate Editor: Jonathan Wren

Received on April 3, 2009; revised on June 24, 2009; accepted on July 16, 2009

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