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Bioinformatics Advance Access published online on November 16, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti142
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received August 17, 2004
Revised November 4, 2004
Accepted November 5, 2004

Applications note

Multiple sequence alignment with user-defined constraints @ 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

1 Universität Göttingen, Institut für Mikrobiologie und Genetik, Abteilung für Bioinformatik, Goldschmidtstr. 1, D-37077 Göttingen, Germany
2 Universität Leipzig, Institut für Informatik und Interdisziplinäres Zentrum für Bioinformatik, Kreuzstrasse 7b, D-04103 Leipzig, Germany
3 Universität Tübingen, Wilhelm-Schickard-Institut für Informatik, Sand 13, D-72076 Tübingen, Germany

* To whom correspondence should be addressed.
Burkhard Morgenstern, E-mail: burkhard{at}gobics.de


  Abstract

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 relations among the input sequences more accurately than fully automated procedures can do.

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


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