TY  - JOUR
A1  - Blakesley, Robert W.
A1  - Hansen, Nancy F.
A1  - Mullikin, James C.
A1  - Thomas, Pamela J.
A1  - McDowell, Jennifer C.
A1  - Maskeri, Baishali
A1  - Young, Alice C.
A1  - Benjamin, Beatrice
A1  - Brooks, Shelise Y.
A1  - Coleman, Bradley I.
A1  - Gupta, Jyoti
A1  - Ho, Shi-Ling
A1  - Karlins, Eric M.
A1  - Maduro, Quino L.
A1  - Stantripop, Sirintorn
A1  - Tsurgeon, Cyrus
A1  - Vogt, Jennifer L.
A1  - Walker, Michelle A.
A1  - Masiello, Catherine A.
A1  - Guan, Xiaobin
A1  - NISC Comparative Sequencing Program
A1  - Bouffard, Gerard G.
A1  - Green, Eric D.
T1  - An intermediate grade of finished genomic sequence suitable for comparative analyses
Y1  - 2004/11/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 2235 
EP  - 2244 
DO  - 10.1101/gr.2648404 
VL  - 14 
IS  - 11 
UR  - http://genome.cshlp.org/content/14/11/2235.abstract 
N2  - 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 ∼40-fold less reagents and ∼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. 
ER  -