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General Genomic Databases

General Genomic Databases

W. M. Keck Center for Genome Informatics

The Keck Center for Genome Informatics WWW server at the Institute of Biosciences and Technology, Texas A & M University, is dedicated to providing an interface to genome databases. It is presently under development. The server currently includes AGsDB, AAnDB, Domestic Animals, Crops and Genome Topographer databases. Database search capabilities are derived from the ACEDB search software.

GenomeNet WWW server

GenomeNet is a Japanese computer network for genome research and related research areas in molecular and cellular biology. GenomeNet was established in September 1991 under the Human Genome Project of the Ministry of Education, Science and Culture. It is operated jointly by the Human Genome Center (HGC), Institute of Medical Science, the University of Tokyo and the Supercomputer Laboratory (SCL), Institute for Chemical Research, Kyoto University, in close cooperation with TISN and WIDE computer network groups in Japan. GenomeNet has a backbone link from Tokyo to Kyoto to Fukuoka. An increasing number of institutions are connected to both the Kyoto and Tokyo centers either by leased lines or ISDN.

HGC and SCL jointly provide database services that are publicly available through GenomeNet. These services may be accessed by e-mail, on-line guest accounts, anonymous FTP, Gopher, WWW, and special client programs. The services include BLAST and FASTA for sequence similarity search, MOTIF for protein sequence motif search, DBGET, IRx, and Entrez for database retrieval. The WWW version of DBGET provides an integrated database search with hot links among a number of databases. In addition, new database systems developed by HGC and unique databases contributed from the Japanese research community are also made available under the GenomeNet services.

The Mammary Transgene Database

This site is provided by Sinai Yarus at the Molecular Biology Computational Resource at Baylor College of Medicine. The Mammary Transgene Database summarizes the results of experiments in which transgenes are expressed in the mammary gland of experimental and agricultural animals. The results of this experiment, details on the transgenes used, and literature references are included.

Whitehead Institute Center for Genome Research

"We are interested in a problem that is closely related to the theme of this workshop, namely, the construction of genome information systems using modular, 'plug-and-play' components. By 'genome information systems' we mean the sorts of computer systems constructed at genome centers, as well as organism-specific data resources and other public data repositories. By 'components' we mean significant subsystems, such as databases, analysis programs, and user interfaces."

"At present, almost all genome information systems are constructed from scratch with little reuse of software developed elsewhere. The main exceptions are a few organism-specific data resources that have adopted a complete existing system, generally ACEDB, and use it with minor customization. In other words, the choices that face the architect of a genome information system today are: (i) build it yourself so that it does exactly what you want, or (ii) adopt someone else's system and live with most of its quirks and limitations. There is no middle ground in which a designer could choose to build some parts of the system, while adopting existing components for the remainder."

Washington University Institute for Biomedical Computing

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