Journal Article

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

Carsten Kemena and Cedric Notredame

in Bioinformatics

Volume 25, issue 19, pages 2455-2465
Published in print October 2009 | ISSN: 1367-4803
Published online July 2009 | e-ISSN: 1460-2059 | DOI:

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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.


Journal Article.  10078 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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