International Bioinformatics Database Institutions

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:

Create automated systems for storing and analyzing knowledge about molecular biology, biochemistry, and genetics;
Perform research into advanced methods of computer-based information processing for analyzing the structure and function of biologically important molecules;
Facilitate the use of databases and software by biotechnology researchers and medical personnel; and
Coordinate efforts to gather biotechnology information worldwide.

The NCBI has implemented its four goals through the following programs. NCBI assumed responsibility for the GenBank DNA sequence database in October, 1992. At the NLM, specially trained indexers with graduate-level biology experience create sequence data records from the scientific literature. This information is augmented by data submissions directly from authors. Collaborations and exchange of data exist with the international nucleotide databases, European Molecular Biology Laboratory (EMBL) and the DNA Database of Japan (DDBJ). A program for sequence similarity searching developed at NCBI, called BLAST, is being used by over 80 major sequencing centers to execute network sequence searches against the entire DNA database in less than 15 seconds. Complementing the network services, databases and software on CD-ROMs permit standalone access to subsets of databases on investigators' own desktop workstations. A CD-ROM, Entrez: Sequences, is being distributed for end-user access to an integrated view of sequence and bibliographic data. NCBI e-mail servers provide an alternative way to retrieve sequences by similarity or full-text searching. In conjunction with the NLM's Library Operations Division, monthly literature surveillance is provided to research databanks such as PIR and the Genome Data Bank. The NCBI assists in the cross-indexing of related molecular biology databases in MEDLINE and has developed the text retrieval software (IRX ) for OMIM. IRX also supports access intramurally at NIH by several hundred users to 15 sequence and factual databases.

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).

ExPASy Molecular Biology Server

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

DDBJ (DNA Data Bank of Japan)

We, DDBJ, began a DNA data bank activity in Japan in 1984 with endorsements of the Ministry of Education, Science, and Culture and representative Japanese molecular biologists. From the beginning, it was intended that DDBJ should be operating as one of the International DNA Databases including EBI (European Bioinformatics Institute; responsible for EMBL database) in Europe and NCBI (National Center for Biotechnology Information; responsible for GenBank database) in the USA as the two other members.

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.

E-mail address for inquiries : ddbj@ddbj.nig.ac.jp
E-mail address for data submission: ddbjsub@ddbj.nig.ac.jp
E-mail address for citation update: ddbjupdt@ddbj.nig.ac.jp

DDBJ (DNA Data Bank ofJapan) Network Servers

Following 8 servers are available at DDBJ.

     Anonymous ftp server:

          ftp.nig.ac.jp (133.39.3.6)

          (README of ftp service)

     WAIS server:

          (:source
          :version 3
          :ip-address "133.39.3.6"
          :ip-name "wais.nig.ac.jp"
          :tcp-port 210
          :database-name "dna"
          :cost 0.00
          :cost-unit :free
          :maintainer "ddbj@ddbj.nig.ac.jp"
          :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:

          fasta@nig.ac.jp
          Send E-mail to fasta@nig.ac.jp with the word "help" in the mail
          body.  You will get brief help message from this server.

     Blast E-mail server:

          blast@nig.ac.jp
          Send E-mail to blast@nig.ac.jp with the word "help" in the mail
          body.  You will get brief help message from this server.

     malign E-mail server:

          malign@nig.ac.jp
          Send E-mail to malign@nig.ac.jp with the word "help" in the mail
          body.  You will get brief help message from this server.

     get-entry E-mail server:

          get-entry@nig.ac.jp
          Send E-mail to get-entry@nig.ac.jp 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:

     ddbjupdt@ddbj.nig.ac.jp

     and the data will be released to the server as soon as possible.

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