Skip Navigation

This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Fasulo, D.
Right arrow Articles by Mobarry, C.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Fasulo, D.
Right arrow Articles by Mobarry, C.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics Vol. 18 no. 90001 2002
Pages S294-S302
© 2002 Oxford University Press

Efficiently detecting polymorphisms during the fragment assembly process

Daniel Fasulo , Aaron Halpern , Ian Dew and Clark Mobarry

Informatics Research, Celera Genomics, 45 W. Gude Dr., Rockville MD 20850, USA

Received on January 24, 2002 ; revised on March 28, 2002 ; accepted on March 28, 2002

Motivation: Current genomic sequence assemblers assume that the input data is derived from a single, homogeneous source. However, recent whole-genome shotgun sequencing projects have violated this assumption, resulting in input fragments covering the same region of the genome whose sequences differ due to polymorphic variation in the population. While single-nucleotide polymorphisms (SNPs) do not pose a significant problem to state-of-the-art assembly methods, these methods do not handle insertion/deletion (indel) polymorphisms of more than a few bases.

Results: This paper describes an efficient method for detecting sequence discrepencies due to polymorphism that avoids resorting to global use of more costly, less stringent affine sequence alignments. Instead, the algorithm uses graph-based methods to determine the small set of fragments involved in each polymorphism and performs more sophisticated alignments only among fragments in that set. Results from the incorporation of this method into the Celera Assembler are reported for the D. melanogaster, H. sapiens, and M. musculus genomes.

Availability: The method described herein does not constitute a stand-alone software application, but is laid out in sufficient detail to be implemented as a component of any genomic sequence assembler.

Contact: daniel.fasulo{at}celera.com

Keywords: whole-genome assembly; shotgun sequencing; polymorphism.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Genome Res.Home page
M. Pop, D. S. Kosack, and S. L. Salzberg
Hierarchical Scaffolding With Bambus
Genome Res., January 1, 2004; 14(1): 149 - 159.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.