Publications - Published papers

Please find below publications of our group. Currently, we list 563 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

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Multiple sequence alignment with user-defined anchor points

Burkhard Morgenstern, Sonja J. Prohaska, Dirk Pohler, Peter F. Stadler


PREPRINT 06-025: [ PDF ]  [ PS ]
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Status: Published

Alg.Mol.Biol. 1:6 (2006).


In many situations, automated multi-alignment programs are not able to correctly align families of nucleic acid or protein sequences. Difficult cases comprise not only distantly related sequences but also tandem duplications independent of their evolutionary age. Frequently, additional biological information is available that establishes homologies at least in parts of the sequences based on structural or functional consideration. In the present paper, we describe a semi-automatic approach to multiple sequence alignment in which the user can explicitly 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 that respects these user-defined constraints and hence should be biologically more plausible than alignments produced by fully automated procedures. We apply our approach to genomic sequences adjacent to the Hox genes. As a by-product, we obtain not only useful insights for the further development of alignment algorithms, but also an improved approach to phylogenetic footprinting.


multiple sequence alignments, anchored alignments, Hox gene clusters, phylogenetic footprinting


Updated from: Burkhard Morgenstern, Sonja J. Prohaska, Nadine Werner, Jan Weyer-Menkhoff, Isabelle Schneider, Amarendran R. Subramanian, Peter F. Stadler,In: Robert Giegerich and Jens Stoye (eds), German Conference on Bioinformatics 2004, pp. 25-36 (2004)