Akira Ohyama

Point matching under non-uniform distortions

This paper discusses the pattern matching problem for points under non-uniform distortions, which arises from the analysis of two-dimensional (2-D) electrophoresis images. First, we provide a formal definition of the problem. Next, we prove that it is NP-hard in two (or more) dimensions. This proof is based on a reduction from planar 3SAT. Then we present a simple polynomial time algorithm for a special and one-dimensional case of the problem, which is based on dynamic programming. We also present a practical heuristic algorithm for identifying a match between two sets of spots in 2-D gel electrophoresis images obtained from genomic DNA.

Matching of Spots in 2D Electrophoresis Images. Point Matching Under Non-uniform Distortions

In this paper, we study pattern matching of points under non-uniform distortions. First we give a natural definition for the problem. Next we present a simple polynomial time algorithm for the one-dimensional case of the problem, whereas we prove that it is NP-hard in two (or more) dimensions. Then we present a practical heuristic algorithm for finding a matching between two sets of spots obtained by the two-dimensional gel electrophoresis technique, which is a special but important case of the problem.

Management System for Sequencing Data of Human Genome

ALIS (Advanced Life science Information Systems) is dedicated to supporting and encouraging large scale human genome research by creating and distributing databases and providing the computing environment. We report on the primary status of ALIS project and our WWW service site ( http://www-alis.tokyo.jst-c.go.jp ). The primary stage of the project has three aspects: large-scale human genome sequencing, construction of an integrated human genome database and development of supporting function for the database.

An Integrated System for Large-Scale Sequencing: Dr. AGCT

We have developed a set of tools for large scale sequence analysis, Dr.AGCT. MAEditor can incorporate the outputs from other assembly software and it can also be used to display a single trace from both ABI and ALF sequencers. Sequence quality control is the most important feature of Dr.AGCT. Other project monitoring systems are also used to reduce the human intervention in several steps of sequencing process. 1 System Description Current methods of large scale sequence analysis involve the use of various set of software such as database homology searching and fragment assembly. We have developed a set of tools that can be useful for random sequencing and utilize the results of different programs such as GCG, XGAP or SHOTGUN. MAEditor has two mode. One is used to display and edit the contigs assembled by other software then create the contigs that can be reassembled by other software (Figure 1) and the other is used to manage a single trace data from ABI or ALF sequencers. The trace data can be seen in a way as one line or as several lines (Figure 2). The multiple line mode is useful to see the sequence as a whole. Sequence quality can be calculated by using Staden or other methods, and displayed graphically to check the accuracy of the base. 1王 忠 清 , 宮 嶋伸 行:か ず さDNA研 究 所,〒292千 葉 県木 更津 市 矢那 内 野1532-3 2大 山 彰 :三 井 情 報 開 発(株)〒102千 代 田 区麹 町3 -7-4