ALIS: Data Management Systems
for Human Genome Sequencing

Mika Hirakawa
Junko Shimada

Kensaku Imai
Hiroko Yamaguchi
yamako@tokyo.jst.go.jp
Kazuo Takehana
Katsuji Matsumura
sjunko@tokyo.jst.go.jp
take3@tokyo.jst.go.jp
katsuji@tokyo.jst.go.jp
Takehiko Itoh
Masako Kuroda
mika@tokyo.jst.go.jp

imai@tokyo.jst.go.jp

takehiko@tokyo.jst.go.jp

kuroda@jst.go.jp

Bioinformatics division, Advanced Databases Department
Japan Science and Technology Corporation (JST)1 Introduction
The ALIS (the Advanced Lifescience Information Systems) Project has commissioned four laboratories
to execute sequencing of human genome regions to demonstrate the feasibility of large-scale humangenome sequencing in Japan. The sequence data of genome project should be release as soon as
possible with mapping information on an international consensus, so the mission of JST is acquisition
all of data from the ALIS sequencing project and publishes data by our web. Our systems areable to process sequencing information for web publication with automatically drawn maps. Largescale human genome sequencing will be more common strategy to search genes by improvement oftechnology for sequencing. ALIS sequencing management systems will apply to acquire mega-scaled
human genome sequences for biological researches in general laboratories.

2 Data acquisition
Since 1995, the JST ALIS (Advanced Life Science Information Systems) Project has acquired contiguous mega-scale sequences of human genome. JST gave four laboratories, which have a principal
investigator with the motivation to sequence the human genome through more than 1 mega-bases,
commissions to execute large-scale sequencing of the human. This rst attempt of generation datais going well and about 15 million bases are sequenced by the March 1999. Sequencing is conducted
at individual laboratories, with strategies determined by each site. There are many varieties evenin same kinds of data, because of di erences of sequencers, software and their conditions. We havebeen working on the acquisition of data from the laboratories and designing a database to maintainit. At rst we design a master database to treat the data from each sequencing team equally. The
database stores experimental sequencing data and information to identify the target regions, sources
and investigators in the team. Sequencing data from each laboratory consist of consensus sequences ofeach clone and continuous regions, results of assembly of fragment data and sequence traces by MOs
and tapes. The data collection system checks all data by check algorithm to evaluate their le formats
and data types to determine whether or not they can be registered into the database. The system uses
SYBASE as DBMS for the master database. The system also post-processes among registered data
to give relational information. The data except from storage media is entered through Web interfaces.
Pre-viewer on Web is available for maintenance of map information. DNA markers and found genes
are annotated on sequences by using marker search programs.
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Figure 1: Image of ALIS Sequencing Management Systems

3 Data publication
Data publication system has another database to manage data used for WWW pages. All the web
pages are generated by perl scripts automatically with the data from the database. The databasemanages and maintains data by the region and release date. ALIS Human Genome Sequencing
Pages provide three features of maps for target regions nished nucleic acid sequences and pro le ofsequencing sites. All the mapped objects have links to reach detail information. There are three ways
to see maps and sequences from top-page, selecting a link of chromosome, band of target regions andsequencing team. The top-page also has direct link to download sequence data.

4 Prospect
Using ALIS data management systems will be able to acquire any sequence data in the les suited
to our directory structure. Improvement of sequencing technology makes easier to get mega-scaled
sequence data, so it will be power-full strategy to search genes in near future. On the other sidemega-scaled sequencing generates huge data, so it is not easy to manage and release data in general
biological laboratories. Our system will be able to support such a mega-scaled biological sequencing
projects.

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