Publications - Published papers

Please find below publications of our group. Currently, we list 508 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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Progressive sequence alignments from Triplets

Matthias Kruspe, Peter F. Stadler


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BMC Bioinformatics 8: 254 (2007)


<b>Motivation:</b> The quality of progressive sequence alignments strongly depends on the accuracy of the individual pairwise alignment steps since gaps that are introduced at one step cannot be removed at later aggregation steps. Adjacent insertions and deletions necessarily appear in arbitrary order in pairwise alignments and hence form an unavoidable source of errors. <br> <b>Idea:</b> Here we present a modified variant of progressive sequence alignments that addresses both issues. Instead of pairwise alignments we use exact dynamic programming to align sequence or profile triples. This avoids a large fractions of the ambiguities arising in pairwise alignments. In the subsequent aggregation steps we follow the logic of the Neighbor-Net algorithm, which constructs a phylogenetic network by step-wisely replacing triples by pairs instead of combining pairs to singletons. To this end the three-way alignments are subdivided into two partial alignments, at which stage all-gap columns are naturally removed. This alleviates the ``once a gap, always a gap&#039;&#039; problem of progressive alignment procedures. <br> <b>Results:</b> The three-way Neighbor-Net based alignment program <tt>aln3nn</tt> is shown to compare favorably on both protein sequences and nucleic acids sequences to other progressive alignment tools. In the latter case one easily can include scoring terms that consider secondary structure features. Overall, the quality of resulting alignments in general exceeds that of <tt>clustalw</tt> or other multiple alignments tools even though our software does not included heuristics for context dependent (mis)match scores. <br> <b>Availability:</b> The Software is freely available for download from <a href=""><tt></tt></a>