title: CombAlign: a protein sequence comparison algorithm considering recombinations.
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.
authors.affiliation: EML Research, Schloss-Wolfsbrunnenweg 33, D-69118 Heidelberg, Germany. wegner@eml-r.villa-bosch.de
authors.forename: Katja
authors.initials: K
authors.lastname: Wegner
authors.forename: Stephan
authors.initials: S
authors.lastname: Jansen
authors.forename: Stefan
authors.initials: S
authors.lastname: Wuchty
authors.forename: Ralph
authors.initials: R
authors.lastname: Gauges
authors.forename: Ursula
authors.initials: U
authors.lastname: Kummer
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D011995:Recombination, Genetic; D020539:Sequence Analysis, Protein
chemical_list: D011506:Proteins