Multiple Alignment of Biological Sequences Containing Tandem Repeat

Hidetoshi Kitada [1] (
Kazuhiro Tono [1] (
Masahito Yamamoto [1] (
Tamotsu Mitamura [1] (
Azuma Ohuchi [1] (
Toshio ohyanagi [2] (
Norio Matsushima [2] (

[1] Division of Systems and Information Engineering,
Faculty of Engineering, Hokkaido University
Kita 13, Nishi 8, Kita-ku, Sapporo, Hokkaido 060, Japan
[2] School of Health Sciences,
Sapporo Medical University
Minami 1, Nishi 17, Chuou-ku, Sapporo, Hokkaido 064, Japan


Multiple sequence alignment can be a useful technique for studying molecular evolution and analyzing sequence-structure relationships. The multiple sequence alignment problem may be formulated as an optimization problem and various approaches to solving it have been applied in the past. But when the sequence contains tandem repeat, the conventional methods cannot yield the biologically significant alignment. We present a method for the multiple alignment of sequences containing tandem repeat.