Knowledge Discovery from Genome Databases

基因组序列的阐明正在进行中。我们已经开发了一些算法来有效地处理大规模的基因组序列，以获得新的见解生物过程。这些研究活动的主要成果总结如下：1.高特异性基因组PCR引物的设计及其在黑猩猩Y染色体分析中的应用研究进展.研究和开发设计siRNA序列，以特异性敲除感兴趣的基因，而不影响脱靶基因。这些结果可通过万维网http：//designmai.jp/查阅，该网站已被广泛使用。研究和开发用于分析5 'SAGE标签信息的软件程序。由于5 'SAGE标签提供了转录起始位点的信息，我们利用5' SAGE标签预测基因组序列中的基因编码区.全基因组鸟枪法序列片段拼接软件的研究与开发。该软件被用来制作青鳉鱼和蚕的基因组序列草图。研究和开发用于大规模基因组序列比较的高效算法.利用青鳉、河豚、斑马鱼、人类和鸡的基因组对脊椎动物基因组进化进行了研究，提出了脊椎动物基因组进化的新设想.研究和开发从基因组中提取重复序列的算法。该软件在检测新的重复序列方面是有效的，我们已经使用它从青鳉基因组中发现了128个重复序列。研究和开发结合聚类和分类思想的新的数据挖掘算法。及其在基因表达数据分析中的应用.蛋白质编码区预测新算法的研究与开发.利用果蝇翅显微图像处理软件研究细胞增殖调控基因。

The elucidation of genomic sequences is ongoing. We have developed a number of algorithms for processing large-scale genomic sequences efficiently in order for deriving new insights into biological process. The major outcomes of these research activities are summarized as follows:1. Research and development of designing highly specific genomic PCR primers and its application to the analysis of Chimpanzee Y chromosome.2. Research and development of designing siRNA sequences to knockdown genes of interest specifically without affecting off-target genes. The results have been available through the WWW at http://designmai.jp/, which has been widely used.3. Research and development of software programs for analyzing 5'SAGE tag information. Since 5'SAGE tags provide transcription start site information, we utilized 5'SAGE tags to predict gene coding regions in genomic sequences.4. Research and development of software programs for assembling whole genome shotgun sequence fragments. The software was used to produce draft genome sequences for medaka fish and silkworm.5. Research and development of efficient algorithms for comparing large-scale genomic sequences.6. Elucidation of vertebrate genome evolution using the genomes of medaka, Tetraodon, zebrafish, humans, and chicken, which yielded novel scenario of vertebrate genome evolution.7. Research and development of algorithms for extracting repetitive sequences from a genome. This software is effective in detecting novel repeat sequences, and we have used it to uncover 128 repeat sequences from the medaka genome.8. Research and development of new data mining algorithm that combines the ideas of clustering and classification., and its application to the analysis of gene expression data.9. Research and development of novel algorithm for predicting protein coding regions.10. Research of image processing software for micrographs of fruitfly wings to study genes of controlling cell proliferation.