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，有效地处理大规模基因组序列，以获得对生物过程的新见解。这些研究活动的主要成果总结如下：1。高特异性基因组PCR引物设计研究进展及其在黑猩猩Y染色体分析中的应用[j]。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的研究和发展。研究结果可通过广泛使用的WWW （http://designmai.jp/）获得。5′sage标签信息分析软件程序的研究与开发。由于5'SAGE标签提供了转录起始位点信息，我们利用5'SAGE标签来预测基因组序列中的基因编码区域。全基因组霰弹枪序列片段组装软件程序的研究与开发。该软件被用于制作medaka鱼和蚕的基因组序列草图。大规模基因组序列比较的高效算法研究与发展。利用medaka、Tetraodon、斑马鱼、人类和鸡的基因组对脊椎动物基因组进化的阐释，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，我们已经用它从medaka基因组中发现了128个重复序列。研究和开发结合了聚类和分类思想的新数据挖掘算法。，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发展。果蝇翅膀显微图像处理软件研究控制细胞增殖的基因。

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.