Send to

Choose Destination
IEEE/ACM Trans Comput Biol Bioinform. 2006 Oct-Dec;3(4):395-407.

Comparing tandem repeats with duplications and excisions of variable degree.

Author information

Faculty of Technology, Bielefeld University, Germany.


Traditional sequence comparison by alignment employs a mutation model comprised of two events, substitutions and indels (insertions or deletions) of single positions. However, modern genetic analysis knows a variety of more complex mutation events (e.g., duplications, excisions, and rearrangements), especially regarding DNA. With ever more DNA sequence data becoming available, the need to accurately compare sequences which have clearly undergone more complicated types of mutational processes is becoming critical. Herein we introduce a new method for pairwise alignment and comparison of sequences with respect to the special evolution of tandem repeats: substitutions and indels of single positions and, additionally, duplications and excisions of variable degree (i.e., of one or more repeat copies simultaneously) are taken into account. To evaluate our method, we apply it to the spa VNTR (variable number of tandem repeats) cluster of Staphylococcus aureus, a bacterium of high medical importance.

[Indexed for MEDLINE]

Supplemental Content

Full text links

Icon for IEEE Engineering in Medicine and Biology Society
Loading ...
Support Center