The NCBI is responsible for building, maintaining, and distributing GenBank, the NIH genetic sequence database that collects all known DNA sequences from scientists worldwide. The NCBI is a division of the National Library of Medicine (NLM) and is located on the campus of the National Institutes of Health (NIH) in Bethesda, Maryland. The late Senator Claude Pepper recognized the importance of computerized information processing methods for the conduct of biomedical research and sponsored legislation that established in November, 1988, the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM). The NLM was chosen because it had experience in creating and maintaining biomedical databases and because, as part of the National Institutes of Health (NIH), it could establish an intramural research program in computational molecular biology. NCBI's mission is to develop new information technologies to aid in the understanding of fundamental molecular and genetic processes that control health and disease. Its mandate includes four major tasks:
Go to the NCBI Home Page
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. 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.
Go to the GenomeNet Home Page
This is the world-wide web (WWW) server of the European Bioinformatics Institute (EBI)which is located at Hinxton Hall near Cambridge in the UK. The EBI is an Outstation of the European Molecular Biology Laboratory (EMBL). EMBL was established in 1974 and is supported by 14 European countries and Israel. EMBL consists of a main Laboratory in Heidelberg (Germany) and three Outstations in Hamburg (Germany), Grenoble (France) and Hinxton (Great Britain). As an institute with excellent facilities, EMBL prides itself on its intellectually open and challenging atmosphere, which encourages innovation and collaboration. The science performed here is first rate. Yet, in the long-term, the scientific networks created by the scientists who pass through EMBL play an equally more important role in the development of our international scientific environment, by transmitting EMBL's techniques and philosophy throughout its Member States. The current research activities of the main Laboratory are carried out in four main Research Programmes, each consisting of several independent groups focussing on a specific area of molecular and cell biology. Two Instrumentation Programmes develop equipment, technology and techniques for these fields. Through its Outstations in Hamburg and Grenoble, EMBL provides European scientists with access to highly intensive X-rays and neutron radiation for structural studies. The Hinxton Oustation specialises in research and service in the field of bioinformatics.
Go to the EBI (European Bioinformatics Institute) Home Page
Go to Sanders Home Page at EMBL (Protein Modeling).
The ExPASy World Wide Web (WWW) molecular biology server of the Geneva University Hospital and the University of Geneva is dedicated to the analysis of protein and nucleic acid sequences as well as 2-D PAGE. It allows you to browse through a number of databases produced in Geneva, such as SWISS-PROT, PROSITE, SWISS-2DPAGE, SWISS-3DIMAGE and SeqAnalRef, as well as other cross-referenced databases (such as EMBL/GenBank, OMIM, Medline, FlyBase, LISTA, YEPD, SubtiList, etc). It also allows access to various documents and sequence analysis tools.
Go to the ExPASy Molecular Biology Server at the University of Geneva
Consequently, we have been collaborating with these data banks in many aspects by daily exchange of messages and data through international networks, and by holding two annual meetings, the International DNA DataBanks Advisory Meeting and the International DNA Data Banks Collaborative Meeting.
DDBJ is the sole DNA data bank in Japan, which is officially certified to collect DNA sequences from researchers and which can issue accession numbers to the data submitters. We collect data mainly from Japanese researchers, but of course accept data and issue accession numbers to researchers in any other countries. We exchange the collected data with EMBL/EBI and GenBank/NCBI on daily base, so that the data banks share virtually the same data at any moment.
Following 8 servers are available at DDBJ. Anonymous ftp server: ftp.nig.ac.jp (188.8.131.52) (README of ftp service) WAIS server: (:source :version 3 :ip-address "184.108.40.206" :ip-name "wais.nig.ac.jp" :tcp-port 210 :database-name "dna" :cost 0.00 :cost-unit :free :maintainer "firstname.lastname@example.org" :subjects "DNA sequences (DDBJ/EMBL/GenBank) including daily updates" :description "Server created with WAIS release 8 b5 (iubio-wais) on Dec 4 12:20:57 1992 by dbm@night This server is off on Sunday The files of type dna used in the index were: /ftp/dna " ) Gopher server: Name=DNA Data Bank of Japan, National Institute of Genetics, Mishima Type=1 Port=70 Path= Host=gopher.nig.ac.jp Fasta E-mail server: email@example.com Send E-mail to firstname.lastname@example.org with the word "help" in the mail body. You will get brief help message from this server. Blast E-mail server: email@example.com Send E-mail to firstname.lastname@example.org with the word "help" in the mail body. You will get brief help message from this server. malign E-mail server: email@example.com Send E-mail to firstname.lastname@example.org with the word "help" in the mail body. You will get brief help message from this server. get-entry E-mail server: email@example.com Send E-mail to firstname.lastname@example.org with the word "help" in the mail body. You will get brief help message in Japanese from this server. WWW (World Wide Web) server: http://www.nig.ac.jp NOTE: THE WWW SERVER provides only documentation, not searching ability DNA sequence files are located by its ACCESSION number. Currently, you can not find sequence by its secondary accession number. For example, you can find D00066 in /dna/D/00/06/D00066 directory. ftp> cd /dna/D/00/06/D00066 250 CWD command successful. ftp> ls -la 200 PORT command successful. 150 Opening ASCII mode data connection for /bin/ls. total 20 drwxr-xr-x 2 dbm 512 Aug 28 02:13 . drwxr-xr-x 11 dbm 512 Aug 27 13:56 .. -rw-r--r-- 1 dbm 5934 Aug 27 08:41 D00066.D -rw-r--r-- 1 dbm 4784 Aug 28 02:13 D00066.E -rw-r--r-- 1 dbm 6240 Aug 27 16:42 D00066.L 226 Transfer complete. remote: -la 272 bytes received in 1.1 seconds (0.24 Kbytes/s) An extension character, D,E,L,N shows the data source. For example, D00066.D is from DDBJ, D00066.E is from EMBL data lib., D00066.L(N) is from GenBank. IF YOU DO NOT FIND THE ACCESSION NUMBER ON THE SERVER: Some authors request that data be held in confidence until after publication even though they have already been assigned an accession number for their data. This causes an additional delay in data release because the databank staff must ascertain that the data have appeared in print. If you have a reference to sequence data but can not retrieve the data from the server, please send the literature reference and accession number (or locus name) to: email@example.com and the data will be released to the server as soon as possible.
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