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Bioinformatics Advance Access originally published online on November 16, 2004
Bioinformatics 2005 21(7):1271-1273; doi:10.1093/bioinformatics/bti142
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Published by Oxford University Press 2004.

Multiple sequence alignment with user-defined constraints at GOBICS

Burkhard Morgenstern 1,*, Nadine Werner 1, Sonja J. Prohaska 2, Rasmus Steinkamp 1, Isabelle Schneider 1, Amarendran R. Subramanian 3, Peter F. Stadler 2 and Jan Weyer-Menkhoff 1

1Institut für Mikrobiologie und Genetik, Universität Göttingen, Abteilung für Bioinformatik Goldschmidtstraße 1, D-37077 Göttingen, Germany
2Institut für Informatik und Interdisziplinäres Zentrum für Bioinformatik, Universität Leipzig Germany
3Wilhelm-Schickard-Institut für Informatik, Universität Tübingen Sand 13, D-72076 Tübingen, Germany

*To whom correspondence should be addressed.

Summary: Most multi-alignment methods are fully automated, i.e. they are based on a fixed set of mathematical rules. For various reasons, such methods may fail to produce biologically meaningful alignments. Herein, we describe a semi-automatic approach to multiple sequence alignment where biological expert knowledge can be used to influence the alignment procedure. The user can specify parts of the sequences that are biologically related to each other; our software program uses these sites as anchor points and creates a multiple alignment respecting these user-defined constraints. By using known functionally, structurally or evolutionarily related positions of the input sequences as anchor points, our method can produce alignments that reflect the true biological relationships among the input sequences more accurately than fully automated procedures can do.

Availability: Our software is available online at GÖttingen BIoinformatics Compute Server (GOBICS), http://dialign.gobics.de/anchor/index.php

Contact: burkhard{at}gobics.de


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This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
Y.-S. Chung, W.-H. Lee, C. Y. Tang, and C. L. Lu
RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W639 - W644.
[Abstract] [Full Text] [PDF]


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