## Fast A* Algorithms for Multiple Sequence Alignment

Takahiro Ikeda (ike@is.s.u-tokyo.ac.jp)

Hiroshi Imai (imai@is.s.u-tokyo.ac.jp)

Department of Information Science,
Faculty of Science,

University of Tokyo

7-3-1 Hongo, Bunkyo-ku, Tokyo 113, Japan

**Abstract**
The multiple alignment of the sequences of DNA and proteins is
applicable to various important fields in molecular biology.
Although the approach based on Dynamic Programming is well-known for
this problem, it requires enormous time and space to obtain the
optimal alignment. On the other hand, this problem corresponds to
the shortest path problem and the A* algorithm, which can
efficiently find the shortest path with an estimator, is usable.

This paper directly applies the A* algorithm to multiple
sequence alignment problem with more powerful estimator in more than
two dimensional case and discusses the improvement of this approach
utilizing an upper bound of the shortest path length. The algorithm
to provide the upper bound is also proposed in this paper.