|
|
|
|
Contemporary sequence alignment algorithms face limitations in detecting non-order-conserving recombinations, which is due to the basic linear treatment of sequence comparisons. Therefore, 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 resemble 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. The program is available for free for non-commercial use, subject to our licence. Users wanting to use the program in a commercial setting should contact us to arrange a licence for its use. |