Subject: AA sequence databases

From: [email-masked] (Mark Dalton)
Date: Fri, 25 Mar 1994 18:34:33 -0600 (CST)

This is in reply to a request on where to find the databases of
peptide sequences.  I will give a list of where to access most
databases (DNA, RNA, amino acid, etc.) That was compiled by Amos Bairoch). 
Also most of the databases are available via gopher and/or mosaic.

For primary protein sequence databases: PIR and Swiss-prot have been
the most common, there is also GenPept.  Many of the DNA sequences
will also have included with them the protein sequence.

Once you get to one Mosaic server, you are likely to find the rest
in this list and more.

Mosaic (From my hot-list):
http://www.ncbi.nlm.nih.gov/ Fri Mar 25 18:27:41 1994
The National Center for Biotechnology Information (NCBI)
http://www.gdb.org/hopkins.html Fri Mar 25 18:30:09 1994
Hopkins Bio-Informatics Home Page

http://www.genethon.fr/genethon_en.html Fri Feb 18 09:35:00 1994
Welcome to GENETHON WWW server
http://ibc.wustl.edu/ Fri Mar 25 18:24:41 1994
Washington University Institute for Biomedical Computing
gopher://ibc.wustl.edu/1 Sun Mar 13 21:28:46 1994
Div of Biology and Biomedical Sciences Research Book
http://www.nlm.nih.gov/#r&d Sun Mar 13 21:40:26 1994
HyperDOC: The National Library of Medicine (NLM)
http://golgi.harvard.edu/homepage.genome Fri Mar 25 18:26:40 1994
Harvard Biological Laboratories - Genome Research

Feel free to contact me if you have any questions/problems.

Thanks!

Mark

Below is a list of various databases available via anonymous ftp.

==============================================================================
Name   : serv_ftp.txt
Version: 1.00 / February 1, 1993
Concern: List of molecular biology FTP servers for databases and software
Author : Amos Bairoch / Dept. Medical Biochemistry / University of Geneva
         [email-masked]
==============================================================================

B) DATABASES
============

  B1) Databases abbreviations
  ---------------------------

db          Database

5S_RNA      Berlin 5S rRNA db
AIDS-db     Human Retroviruses and HIV viruses compilation of sequences
AIMB-db     Artificial intelligence and molecular biology researchers db
Alu         Alu Sequence db
Blocks      Protein blocks db
Codon       Codon usage tables for the GCG software package
CpGIsle     CpG islands in the human genome db
CCSD        Complex Carbohydrate Structure db
CUTG        Codon usage tables for all major species
DDBJ        DNA Data Bank of Japan
DSSP        Dictionary of Secondary structure of proteins
ECD         Escherichia coli db
EMBL        European Molecular Biology Laboratory nucleotide sequence db
Enzyme      Enzymes nomenclature db
EPD         Eukaryotic Promoter db
EST-db      Expressed Sequence Tag db
FANS_Ref    Functional Analysis of Nucleotide Sequences bibliography
FlyBase     Drosophila Genetic Maps db
GDB         Human Genome db
GenBank     GenBank nucleic acid db
GenPept     Automatic translation of GenBank CDS into protein sequences
HAEMB       Haemophilia B mutations db
Jour_TOC    Table of contents of some biomolecular journals
Kabat       Sequences of proteins of immunological interest
LiMB        Listing of Molecular Biology databases
NGDD        Normalized Gene Designation db
OMIM        Online Mendelian Inheritance in Man
PDB         Protein Data Bank (3D structures)
PIR         Protein Information Resource (NBRF protein sequence db)
PKCDD       Protein kinases catalytic domain db
Plsearch    Automatically generated protein sequence patterns db
Prosite     Dictionary of Protein Sites and Patterns
Rebase      Restriction Enzymes db
RepBase     Prototypic sequences for human repetitive DNA
SeqanalRef  Sequence analysis bibliography
Small_RNA   Compilation of small RNA sequences
Swiss-Prot  Swiss-Prot protein sequence db
T4-Phage    Bacteriophage T4 genome sequence files
TFD         Transcription Factors Relational db
tRNA        Compilation of tRNA sequences and sequences of tRNA genes

  B2) Major FTP servers for databases
  -----------------------------------

Organism : National Center for Biotechnology Information (NCBI)
Name     : NCBI repository
Address  : ncbi.nlm.nih.gov (130.14.20.1)
Contact  : Scott Federhen; [email-masked]

Organism : European Biology Molecular Laboratory
Name     : EMBL Anonymous Ftp Server
Address  : ftp.embl-heidelberg.de (192.54.41.33)
Contact  : Rainer Fuchs; [email-masked]

Organism : Weizmann Institute of Science (EMBnet Israel national node)
Name     : DNA and protein sequence analysis (DAPSAS) ftp server
Address  : sunbcd.weizmann.ac.il (132.76.64.79)
Contact  : Jaime Prilusky; [email-masked]

Organism : Basel Biozentrum Biocomputing server (EMBnet SWISS national node)
Name     : Basel EMBNet ftp server
Address  : bioftp.unibas.ch (131.152.8.1)
Contact  : Reinhard Doelz; [email-masked]

Organism : National Institute of Genetics (Japan)
Name     : National Institute of Genetics ftp server
Address  : ftp.nig.ac.jp (133.39.16.66)
Contact  : Yoshihiro Ugawa; [email-masked]

+-------------------------+--------+------+------+-------+-------+
|  Name                   |  NCBI  | EMBL | Weiz | Basel | Japan |
+-------------------------+--------+------+------+-------+-------+
|                         |        |      |      |       |       |
|  DDBJ                   |        |      |      |       | Yes   |
|  EMBL                   |        |  Yes |  Yes |  Yes  | Yes   |
|  GenBank                |   Yes  |      |  Yes |       | Yes   |
|  SWISS-PROT             |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  PIR                    |        |      |  Yes |  Yes  | Yes   |
|                         |        |      |      |       |       |
+-------------------------+--------+------+------+-------+-------+
|                         |        |      |      |       |       |
|  5S_rRNA                |        |  Yes |  Yes |  Yes  |       |
|  AIDS-db                |   Yes  |      |  Yes |       |       |
|  AIMB-db                |   Yes  |      |  Yes |       |       |
|  Alu                    |        |  Yes |  Yes |  Yes  |       |
|  Blocks                 |   Yes  |  Yes |  Yes |       | Yes   |
|  CpGIsle                |        |  Yes |  Yes |  Yes  |       |
|  CCSD                   |   Yes  |      |      |  Yes  |       |
|  CUTG                   |        |  Yes |  Yes |  Yes  | Yes   |
|  DSSP                   |        |  Yes |  Yes |       |       |
|  ECD                    |        |  Yes |  Yes |  Yes  | Yes   |
|  EcoSeq/Map/Gene        |   Yes  |      |      |       |       |
|  Enzyme                 |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  EPD                    |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  EST-db                 |   Yes  |      |      |  Yes  |       |
|  FANS-Ref               |        |  Yes |  Yes |  Yes  |       |
|  FlyBase                |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  HAEMB                  |        |  Yes |  Yes |  Yes  |       |
|  Jour_TOC               |   Yes  |      |  Yes |  Yes  |       |
|  Kabat                  |   Yes  |      |  Yes |       |       |
|  LiMB                   |   Yes  |  Yes |  Yes |  Yes  |       |
|  NGDD                   |   Yes  |      |      |  Yes  |       |
|  PKCDD                  |   Yes  |  Yes |  Yes |  Yes  |       |
|  Prosite                |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  Rebase                 |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  Repbase                |   Yes  |  Yes |  Yes |  Yes  |       |
|  SeqanalRef             |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  Small_RNA              |        |  Yes |  Yes |  Yes  |       |
|  T4-Phage               |   Yes  |      |  Yes |  Yes  |       |
|  TFD                    |   Yes  |  Yes |  Yes |  Yes  | Yes   |
|  tRNA                   |        |  Yes |  Yes |  Yes  |       |
|                         |        |      |      |       |       |
+-------------------------+--------+------+------+-------+------ +

  B3) Other FTP servers for databases
  -----------------------------------

Organism : University of Geneva / Medical Biochemistry and University Hospital
Name     : ExPASy server
Address  : expasy.hcuge.ch (129.195.254.61)
Databases: Enzyme, EPD, Jour_TOC, Prosite, SeqanalRef, SWISS-PROT
           Directory: /databases
Contact  : Amos Bairoch; [email-masked]

Organism : Department of Molecular biology / Massachussetts General Hospital
Address  : frodo.mgh.harvard.edu (132.183.190.10)
Databases: EMBL, Codon
Contact  : Mike Cherry; [email-masked]

Organism : University of Houston Gene-Server
Address  : ftp.bchs.uh.edu (129.7.2.43)
Databases: PIR
           Directory: /pub/gene-server/pir
Contact  : Dan Davison; [email-masked]

Organism : Indiana University / Biology Department
Name     : IuBio archive for biology
Address  : ftp.bio.indiana.edu (129.79.224.25)
Databases: FlyBase and various other fly databases and stock lists.
           Archive of the BIOSCI newsgroup postings (In directory:
           /usenet/bionet).
Contact  : Don Gilbert; [email-masked]

Organism : ?
Address  : ftp.tigr.org (192.207.234.10)
Databases: EST-db
Contact  : ?

Organism : National Library of Medicine
Address  : lhc.nlm.nih.gov (130.14.1.128)
Databases: AIMB-db
           Directory= /pub/aimb-db
Contact  : Lawrence Hunter; [email-masked]

Organism : Molecular Biology Computer Research Resource (MBCRR)
Address  : mbcrr.harvard.edu (134.174.51.4) 
Databases: Plsearch
           Directory= /MBCRR-Package
Contact  : Temple Smith; [email-masked] 

Organism : Human Genome Data Base / Johns Hopkins University
Address  : mendel.welch.jhu.edu (128.220.59.42)
Databases: GDB, OMIM.
Contact  : GDB User Support; [email-masked]

Organism : Protein Data Bank (PDB)
Address  : pdb.pdb.bnl.gov (130.199.144.1)
Databases: PDB
Contact  : [email-masked].

Organism : The Salk Institute for Biological Studies
Address  : salk-sc2.sdsc.edu (192.31.153.12)
Databases: PKCDD
Contact  : Anne Marie Quinn; [email-masked]

Organism : New England BioLabs (NEB)
Address  : vent.neb.com (192.138.220.2)
Databases: Rebase
           Directory= /pub/rebase
Contact  : Dana Macelis; [email-masked]

Organism : NCI-FCRDC
Address  : fconvx.ncifcrf.gov (129.43.52.4)
Databases: GenPept
           Directory= /pub/genpept
Contact  : Mark A. Gunnell; [email-masked]

Organism : Pittsburgh Supercomputing Center (PSC)
Address  : ftp.psc.edu (128.182.62.148)
Databases: GenBank
           Directory= /biomed/genbank/annotated
Contact  : Alex Ropelewski; [email-masked]

Organism : BIOSCI at IntelliGenetics
Address  : net.bio.net (134.172.2.69)
Databases: BIOSCI documents (including FAQ)
           Directory= /pub/BIOSCI
Contact  : Dave Kristofferson; [email-masked]

Organism : SERC Daresbury
Address  : s-crim1.dl.ac.uk (148.79.64.2)
Databases: Various databases and software package. Provides part of what is
           found on the EMBL and INN servers.
Contact  : Alan Bleasby; [email-masked]

==============================================================================

-- 
Mark Dalton                   AUG-GCU-AGA-AAG                  H      
Cray Research, Inc.           M   A   R   K                    |     
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Internet: [email-masked]                                         |   
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