Optimal sequence alignments

Visualization of near-optimal sequence alignments

MOTIVATION Mathematically optimal alignments do not always properly align active site residues or well-recognized structural elements. Most near-optimal sequence alignment algorithms display alternative alignment paths, rather than the conventional residue-by-residue pairwise alignment. Typically, these methods do not provide mechanisms for finding effectively the most biologically meaningful a...

Optimal Alignment of Multiple Sequence Alignments

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 CHAPTER 1: INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . 14 1.1 Perspective . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 1.2 Contributions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 1.3 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ...

Cyclic Sequence Alignments: Approximate Versus Optimal Techniques

The problem of cyclic sequence alignment is considered. Most existing optimal methods for comparing cyclic sequences are very time consuming. For applications where these alignments are intensively used, optimal methods are seldom a feasible choice. The alternative to an exact and costly solution is to use a close-to-optimal but cheaper approach. In previous works, we have presented three subop...

Near-Optimal Block Alignments

In this paper, we improve the idea of the near-optimal alignments. Though the near optimal alignments increase the possibility to find the correct alignment, too many of them may confuse the biologists. So we present the filter scheme for the near-optimal alignments. An easy method to trace the nearoptimal alignments and an algorithm to filter those alignments are proposed.1 The time complexity...

Tools for Fast Sequence Alignments