Murdoch University Research Repository

Welcome to the Murdoch University Research Repository

The Murdoch University Research Repository is an open access digital collection of research
created by Murdoch University staff, researchers and postgraduate students.

Learn more

FBSA: feature-based sequence alignment technique for very large sequences

Bellgard, M. and Kenworthy, W.D. (2003) FBSA: feature-based sequence alignment technique for very large sequences. Applied Bioinformatics, 2 (3). pp. 145-150.

Abstract

The ability to align pairs of very large molecular sequences is essential for a range of comparative genomic studies. However, given the complexity of genomic sequences, it has been difficult to devise a systematic method that can align - even within the same species - pairs of large sequences. Most existing approaches typically attempt to align nucleotide sequences while ignoring valuable features contained within them, eg they filter out low-complexity regions and retroelements before aligning the sequences. However, features are then added post-alignment for visualisation and analysis purposes. We argue that repetitive elements and other features (such as genes, exons and regulatory elements) should be part of the alignment process. A hierarchical approach that aligns the biologically relevant features before aligning the detailed nucleotide sequences has a number of interesting characteristics: (1) features define 'alignment anchor points' that can guide meaningful nucleotide alignment; (2) features can be weighted; (3) a hierarchical approach would identify only meaningful regions to be aligned; (4) nucleotide sequences can be described as sequences of features and non-features, providing a natural mechanism to divide the sequences for processing; and (5) computational speed is significantly faster than other approaches. In this paper, we describe and discuss a feature-based approach to aligning large genome sequences. We refer to this as 'feature-based sequence alignment'.

Item Type: Journal Article
Murdoch Affiliation(s): School of Information Technology
Centre for Comparative Genomics
Publisher: Adis Press
Publisher's Website: http://adisonline.com/bioinformatics/pages/default...
URI: http://researchrepository.murdoch.edu.au/id/eprint/1853
Item Control Page Item Control Page