Construction of an EST database for Bombyx mori

为了为家蚕全基因组分析奠定基础，我们建立了家蚕EST数据库。由于基因表达模式与组织和发育阶段密切相关，我们分析了许多来自不同组织和不同发育阶段的cDNA文库，以覆盖家蚕的全部基因。迄今为止，Bombyx EST数据库包含了来自36个cDNA文库的35000条EST，这些EST被分成约11000条无冗余的EST，平均长度为1.25 kb。与FlyBase的比较表明，目前的EST数据库“SilkBase”覆盖了家蚕所有基因的55%以上。每个cDNA文库中文库特异性ESTs的比例表明我们尚未达到饱和，表明我们构建覆盖所有基因的EST数据库策略的有效性。为了解决即将到来的饱和问题，我们检查了两种方法，减法和归一化，以增加覆盖率和减少管家基因的数量，导致文库特异性ESTs增加了5-11%。通过SilkBase检索，已经出现了许多新基因的鉴定和基因家族的全面克隆。SilkBase与FlyBase和WormBase的直接链接提供了鳞翅目候选特异性基因的快速鉴定。

To build a foundation for the complete genome analysis of Bombyx mori, we have constructed an EST database. Since gene expression patterns deeply depend on tissues as well as developmental stages, we analyzed many cDNA libraries prepared from various tissues and different developmental stages to cover the whole set of Bombyx genes. So far, the Bombyx EST db contains 35,000 ESTs from 36 cDNA libraries, which are grouped into about 11,000 non-redundant ESTs with the average length of 1.25 kb. The comparison with FlyBase suggests that the present EST database, "SilkBase," covers more than 55% of all genes of Bombyx. The fraction of library-specific ESTs in each cDNA library indicates that we have not yet reached saturation, showing the validity of our strategy for constructing an EST database to cover all genes. To tackle the coming saturation problem, we have checked two methods, subtraction and normalization, to increase coverage and decrease the number of housekeeping genes, resulting in 5-11% increase of library-specific ESTs. The identification of a number of novel genes and comprehensive cloning of gene families have already emerged from SilkBase search. Direct links of SilkBase with FlyBase and WormBase provide ready identification of candidate Lepidoptera-specific genes.