Combinatorial algorithms for DNA sequence assembly

Combinatorial algorithms for DNA sequence assembly (1993)

by John D. Kececioglu , Eugene W. Myers

Venue:	Algorithmica
Citations:	33 - 3 self

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Datum	Value	Source
TITLE	Combinatorial algorithms for DNA sequence assembly	user correction - Legacy Corrections
AUTHOR NAME	John D. Kececioglu	SVM HeaderParse 0.1
AUTHOR AFFIL	y	SVM HeaderParse 0.2
AUTHOR NAME	Eugene W. Myers	SVM HeaderParse 0.1
AUTHOR AFFIL	z	SVM HeaderParse 0.2
ABSTRACT	The trend towards very large DNA sequencing projects, such as those being undertaken as part of the human genome initiative, necessitates the development of efficient and precise algorithms for assembling a long DNA sequence from the fragments obtained by shotgun sequencing or other methods. The sequence reconstruction problem that we take as our formulation of DNA sequence assembly is a variation of the shortest common superstring problem, complicated by the presence of sequencing errors and reverse complements of fragments. Since the simpler superstring problem is NP-hard, any efficient reconstruction procedure must resort to heuristics. In this paper, however, a four phase approach based on rigorous design criteria is presented, and has been found to be very accurate in practice. Our method is robust in the sense that it can accommodate high sequencing error rates and list a series of alternate solutions in the event that several appear equally good. Moreover it uses a limited form ...	user correction - Legacy Corrections
YEAR	1993	user correction - Legacy Corrections
VENUE	Algorithmica	INFERENCE
VENUE TYPE	JOURNAL	INFERENCE
PAGES	7--51	INFERENCE
VOLUME	13	INFERENCE
CITATIONS	39 found	ParsCit 1.0