An intermediate grade of finished genomic sequence suitable for comparative analyses
An intermediate grade of finished genomic sequence suitable for comparative analyses
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DOI：
10.1101/gr.2648404
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发表时间：
2004-11-01
期刊：
影响因子：
7
通讯作者：
Green, ED
中科院分区：
文献类型：
--
作者：
Blakesley, RW;Hansen, NF;Green, ED
尽管生成草图质量基因组序列的成本持续下降，但通过“序列整理”过程精炼该序列的成本仍然很高。接近完美的完成序列是人类基因组和一小部分参考基因组的合适目标；然而，至少在可预见的未来，这种高质量的产品无法为大量额外的基因组提供成本证明。在这里，我们描述了一个中级完成的基因组序列（称为比较级完成序列）的产生和质量，这是为多物种序列比较而量身定制的。我们的分析表明，该序列的质量非常高（剩余的间隙和错误大部分落在重复元素内），反映了总序列的99%。重要的是，与生成近乎完美的完成序列（如人类基因组）相比，玉米级序列整理需要的试剂减少了40倍，人员投入减少了10倍。虽然这里应用的是来自单个细菌人工染色体（BAC）克隆的精整序列，但人们可以设想建立常规程序，将来自全基因组霰弹枪测序项目的序列精整到类似的质量水平。迄今为止，我们的经验表明，在进行比较分析的过程中，比较级序列整理是一种实用且经济的选择。
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, cornparative-grade sequence finishing requires similar to40-fold less reagents and similar to10-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.