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Article type: Research Article
Authors: Wegner, Katja | Jansen, Stephan | Wuchty, Stefan | Gauges, Ralph | Kummer, Ursula
Affiliations: EML Research, Schloss-Wolfsbrunnenweg 33, D-69118 Heidelberg, Germany. E-mail: {wegner, gauges, kummer}@eml-r.villa-bosch.de | F. Hoffmann-La Roche Ltd, Grenzacherstr. 124, CH - 4070 Basel, Switzerland. E-mail: [email protected] | Department of Physics, University of Notre Dame 225 Nieuwland Science Hall, Notre Dame, IN 46556, USA. E-mail: [email protected]
Note: [] Corresponding author
Abstract: The basic linear treatment of sequence comparisons limits the ability of contemporary sequence alignment algorithms to detect non-order-conserving recombinations. Here, we introduce the algorithm combAlign which addresses the assessment of pairwise sequence similarity on non-order-conserving recombinations on a large scale. Emphasizing a two-level approach, combAlign first detects locally well conserved subsequences in a target and a source sequence. Subsequently, the relative placement of alignments is mapped to a graph. Concatenating local alignments to reassemble the target sequence to the fullest extent, the maximum scoring path through the graph denotes the best attainable combAlignment. Parameters influencing this process can be set to meet the user's specific demands. combAlign is applied to examples demonstrating the possibility to reflect evolutionary kinship of proteins even if their domains and motifs are strongly rearranged.
Keywords: point mutations, shuffling events, dynamic programming, graph theory, DAG
Journal: In Silico Biology, vol. 4, no. 3, pp. 243-254, 2004
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