Bioinformatics in silico by the Unification of Symobols and Patterns

该项目的开始是为了开发计算智能算法，以发现DNA和氨基酸序列中存在的软模式。主要的方法是在目标。湿生物学家被包括在这个组中，以便抑制过于抽象的问题。基于计算机的信息科学家和基于试管的生命科学家之间的统一仍然需要时间，但是，通过本项目，朝着这种合作迈出了稳步的一步，取得了以下成果：（1）建立了转录起始位点的预测方法。以真核生物的代表人类基因组为研究对象，提出了一种基于支持向量机的谱核、隐马尔可夫模型和快速傅立叶变换相结合的方法。该机制产生了顶级的ROC曲线。在对原核生物的代表大肠杆菌的预测中，将独立成分分析和支持向量机相结合，得到了迄今为止最好的预测效果。(2)提出了一种新的多序列比对算法。此新方法可抑制同一列中出现多个间隙。差距的扩展可以通过分段线性惩罚来调节。整个算法用PRIME软件实现。PRIME在结果对齐和计算速度方面表现出比ClustalW和T-Coffee更好的性能。(3)湿生物学小组在Rad 5l上发现了一个证据，它可以修复被切断的DNA双链。如前所述，本研究在后基因组领域取得了丰硕的成果：启动子和转录起始位点的预测，一种新的多序列比对方法，导致三级结构预测，以及蛋白质功能导致的癌症性质。

This project was started towards the development of computational intelligence algorithms for finding soft patterns existing in DNA and amino acid sequences. The main methodology is in Aim. Wet biologists are included in this group so that overly abstract problems are suppressed. The unification between compute-based information scientists and test-tube-based life scientists still requires time, however, a steady step towards such collaboration was enhanced by this project with the following results :(1) Prediction methods fir the transcription start site were established. On human .genome which is a representative of eukaryotes, a combination of the spectrum kernel, hidden Markov models, and FFT integrated by a support vector machine was presented. This mechanism yielded a top class ROC curves. On the prediction of E.coli which is a representative of prokaryotes, a combination of the independent component analysis and a support vector machine revealed the best prediction performance to date.(2) Anew effective algorithm on the multiple sequence alignment was developed. This new method suppresses the appearance of multiple gaps in the same column. The gap extension can be regulated by piecewise linear penalties. The total algorithm is realized as the software named PRIME. The PRIME showed better performances than ClustalW and T-Coffee in the sense of resulting alignments and computational speed.(3) The wet biology team hind an evidence on Rad5l which repairs cut double strands of DNA. The binding site of Rad51 is altered in breast cancer patients.As was explained above, this research brought about fruitful results on post genome topics : The prediction of promoters and transcription start sites, a new multiple sequence alignment method leading to tertiary structure prediction, and a cancer property caused by protein functions.