List of molecular biology FTP servers (Preliminary edition).
Amos Bairoch
BAIROCH at cmu.unige.ch
Wed Jan 6 20:30:03 EST 1993
==============================================================================
Name : serv_ftp.txt
Version: 0.9 / January 6, 1993
Concern: List of molecular biology FTP servers for databases and software
Author : Amos Bairoch / Dept. Medical Biochemistry / University of Geneva
bairoch at cmu.unige.ch
==============================================================================
-----------------------------------------------------------------------------
THIS IS A PRELIMINARY VERSION OF THIS DOCUMENT, FEEDBACK IN THE FORM
OF CORRECTIONS, ADDITIONS, ETC ARE MORE THAN WELCOME !!!
-----------------------------------------------------------------------------
A) INTRODUCTION
===============
A1) General introduction
------------------------
This document describes the various sources of databases and software for
molecular biologists that are publicly available on the internet computer
network. This documents restricts itself to describing sites that allows
the transfer of files by what is known as anonymous "ftp" (File transfer
protocol). We do not describe here the BIOSCI electronic newsgroup system
or the other bulletin boards that are available to molecular biologist,
nor do we describe email servers. These services are described in the
following documents:
serv_ema.txt: For a list of molecular biology email servers.
serv_bbo.txt: For a list of bulletin boards services for molecular
biologists.
Acknowledgment: the information contained in this document come from many
different sources; but we want to partcularily acknowledge
the work of Michael Gribskov (gribskov at sdsc.edu) which, in
December 1990 and March 1991 produced a compilation of
server sites; Bob Harper (harper at convex.csc.fi) for having
forwarded me information from various sources.
A2) Some tips
-------------
1) On all the FTP servers listed in this document you should login using the
user name "anonymous" and using your full E-mail address as the password
(example: smith at somesite.somenet.node).
2) There are, in general, files with names such as "read.me", "readme.txt"
or "readme" at different directory levels on many FTP servers. If you are
using a server for the first time, it is a good idea to first transfer
these files and to read them before transferring other files. Note that
you can generally do that without interupting the connection by shelling
to your operating system:
a) Type "get readme.txt" to transfer the file on your local system.
b) Once the file has been transferred type "!" (if your local system is
running DOS or UNIX system) or "SPAWN" (if your local system is a VAX
VMS). You will then see your usual operating system prompt.
c) You can then view the file with your favorite file viewer or editor.
d) To get back in the FTP program type "exit" (on DOS or on UNIX) or
"LOGOUT" (on a VAX VMS).
3) When transferring binary files such as program files or compressed files
(with the .Z file extension for example), do not forget to first set the
transfer mode to "binary". Do not also forget to reset it back to "ASCII"
if you later, in the same session, want to transfer text files. However,
if your system is running the same operating system than that of the host
server, you can transfer all files, even text files, in binary mode.
A3) Release history
-------------------
Release 0.9 / January 6, 1993
==============================================================================
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
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; federhen at ncbi.nlm.nih.gov
Organism : European Biology Molecular Laboratory
Name : EMBL Anonymous Ftp Server
Address : ftp.embl-heidelberg.de (192.54.41.33)
Contact : Rainer Fuchs; nethelp at embl-heidelberg.de
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 : James Prilusky; lsprilus at weizmann.weizmann.ac.il
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; doelz at urz.unibas.ch
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; yugawa at genes.nig.ac.jp
+-------------------------+--------+------+------+-------+-------+
| 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 |
| E
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