Inst. f. Informatik   
Uni Leipzig

Bioinformatics Preprint 04-018


Multiple sequence alignment with user-de ned constraints @ GOBICS

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

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Summary: Most multi-alignment methods are fully automated, i.e. they are based on a xed 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 in uence the alignment procedure. The user can specify parts of the sequences that are biologically related to each other; our software program will use these sites as anchor points and create a multiple alignment respecting these user-de ned constraints. By using functionally, structurally or evolutionarily related positions of the input sequences as anchor points, our method can produce alignments that re ect 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), Contact:

Multiple Sequence Alignment, Web Server

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