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, 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.
Blakesley
Robert W
RW
NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
Hansen
Nancy F
NF
Mullikin
James C
JC
Thomas
Pamela J
PJ
McDowell
Jennifer C
JC
Maskeri
Baishali
B
Young
Alice C
AC
Benjamin
Beatrice
B
Brooks
Shelise Y
SY
Coleman
Bradley I
BI
Gupta
Jyoti
J
Ho
Shi-Ling
SL
Karlins
Eric M
EM
Maduro
Quino L
QL
Stantripop
Sirintorn
S
Tsurgeon
Cyrus
C
Vogt
Jennifer L
JL
Walker
Michelle A
MA
Masiello
Catherine A
CA
Guan
Xiaobin
X
Bouffard
Gerard G
GG
Green
Eric D
ED
D000818:Animals; D001483:Base Sequence; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D003001:Cloning, Molecular; D019295:Computational Biology; D020451:Contig Mapping / Q000191:economics* / Q000379:methods; D003365:Costs and Cost Analysis; D030541:Databases, Genetic; D005091:Exons / Q000235:genetics*; D016678:Genome; D007900:Lemur / Q000235:genetics; D008969:Molecular Sequence Data; D010215:Papio / Q000235:genetics; D051381:Rats; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA / Q000191:economics*; D012689:Sequence Homology, Nucleic Acid; D012984:Software / Q000191:economics