Paper Info
Title
Mega weaver: a simple iterative approach for BAC consensus assembly
Abstract
Hierarchical genome assembly can be divided into three distinct stages: Sequencing and assembling shotgun reads for each of a series of selected BAC clones; assembling the resulting fragments into BAC consensus sequences; and mapping and orienting the BAC consensus according to external positional information. We report a new approach for BAC consensus assembly that relies on iterative layouts of overlapping sequence, with no need for prior masking of repetitive sequence. The approach includes major steps of quality filtering and an iterative screening algorithm within and between clusters of overlapping BAC fragments. Each step includes numerous minor steps designed to detect false overlaps at minimal expense in true overlaps In contrast to dynamic algorithms, our approach attempts to minimize false overlaps before attempting to form BAC consensus sequences. We show that false overlaps are reduced to a degree that final BAC consensus assembly is straightforward under a cooordinate system described in the paper. Using human chromosome 22 and a range of simulation conditions, an average of 98.1% false overlaps could be removed, while 6.7% of true overlaps were not detected. The final assembled BAC consensus sequences were nearly optimal, and support the usefulness of our approach for future hierarchical sequencing projects.
Year
Venue
Keywords
2004
APBC
true overlap,bac consensus,bac fragment,approach attempt,simple iterative approach,final bac consensus assembly,mega weaver,false overlap,new approach,selected bac clone,bac consensus assembly,bac consensus sequence,dna sequence,algorithm,assembly
Field
DocType
Citations 
Biology,DNA sequencing,Bioinformatics,Mega-,Consensus sequence,Sequence assembly
Conference
0
PageRank 
References 
Authors
0.34
3
4
Name
Order
Citations
PageRank
Daolong Wang100.68
Mario Lauria262895.12
Bo Yuan3103362.40
Fred A. Wright412712.81