Aligning Two Fragmented Sequences

GS-Aligner: a novel tool for aligning genomic sequences using bit-level operations.

A novel algorithm, GS-Aligner, that uses bit-level operations was developed for aligning genomic sequences. GS-Aligner is efficient in terms of both time and space for aligning two very long genomic sequences and for identifying genomic rearrangements such as translocations and inversions. It is suitable for aligning fairly divergent sequences such as human and mouse genomic sequences. It consi...

Optimal Alignment of Multiple Sequence Alignments

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

OWEN: aligning long collinear regions of genomes

OWEN is an interactive tool for aligning two long DNA sequences that represents similarity between them by a chain of collinear local similarities. OWEN employs several methods for constructing and editing local similarities and for resolving conflicts between them. Alignments of sequences of lengths over 10(6) can often be produced in minutes. OWEN requires memory below 20 L, where L is the su...

A Class Note on Space-Saving Strategies

Straightforward implementation of the dynamic-programming algorithms utilizes quadratic space to produce an optimal global or local alignment. For analysis of long DNA sequences, this space restriction is more crucial than the time constraint. Because of this, different methods have been proposed to reduce the space used for aligning globally or locally two sequences. We first describe a space-...

Kelil Page 1 ALIGNER: Detecting and Aligning Related Protein Sequences ALIGNER: Detecting and Aligning Related Protein Sequences