An intermediate grade of finished genomic sequence suitable for comparative analyses

Although the cost of generating draft-quality genomic sequence continues to decline, refining that sequence by the process of "sequence finishing" remains expensive. Near-perfect finished sequence is an appropriate goal for the human genome and a small set of reference genomes; however, su...

Full description

Saved in:

Bibliographic Details
Published in:	Genome research Vol. 14; no. 11; pp. 2235 - 2244
Main Authors:	Blakesley, Robert W, Hansen, Nancy F, Mullikin, James C, Thomas, Pamela J, McDowell, Jennifer C, Maskeri, Baishali, Young, Alice C, Benjamin, Beatrice, Brooks, Shelise Y, Coleman, Bradley I, Gupta, Jyoti, Ho, Shi-Ling, Karlins, Eric M, Maduro, Quino L, Stantripop, Sirintorn, Tsurgeon, Cyrus, Vogt, Jennifer L, Walker, Michelle A, Masiello, Catherine A, Guan, Xiaobin, Bouffard, Gerard G, Green, Eric D
Format:	Journal Article
Language:	English
Published:	United States Cold Spring Harbor Laboratory Press 01-11-2004
Subjects:	Animals Base Sequence Chromosomes, Artificial, Bacterial - genetics Cloning, Molecular Computational Biology Contig Mapping - economics Contig Mapping - methods Costs and Cost Analysis Databases, Genetic Exons - genetics Genome Lemur - genetics Letters Molecular Sequence Data Papio - genetics Rats Repetitive Sequences, Nucleic Acid Sequence Analysis, DNA - economics Sequence Homology, Nucleic Acid Software - economics
Online Access:	Get full text
Tags:	Add Tag No Tags, Be the first to tag this record!

Description
Summary:	Although the cost of generating draft-quality genomic sequence continues to decline, refining that sequence by the process of "sequence finishing" remains expensive. Near-perfect finished sequence is an appropriate goal for the human genome and a small set of reference genomes; however, such a high-quality product cannot be cost-justified for large numbers of additional genomes, at least for the foreseeable future. Here we describe the generation and quality of an intermediate grade of finished genomic sequence (termed comparative-grade finished sequence), which is tailored for use in multispecies sequence comparisons. Our analyses indicate that this sequence is very high quality (with the residual gaps and errors mostly falling within repetitive elements) and reflects 99% of the total sequence. Importantly, comparative-grade sequence finishing requires approximately 40-fold less reagents and approximately 10-fold less personnel effort compared to the generation of near-perfect finished sequence, such as that produced for the human genome. Although applied here to finishing sequence derived from individual bacterial artificial chromosome (BAC) clones, one could envision establishing routines for refining sequences emanating from whole-genome shotgun sequencing projects to a similar quality level. Our experience to date demonstrates that comparative-grade sequence finishing represents a practical and affordable option for sequence refinement en route to comparative analyses.
Bibliography:	ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 23 These authors contributed equally to this work. Corresponding author. E-mail egreen@nhgri.nih.gov ; fax (301) 402-2040. Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.2648404. Article published online before print in October 2004.
ISSN:	1088-9051 1549-5469
DOI:	10.1101/gr.2648404