AA sequence databases
- From: mwd;at;carina.cray.com (Mark Dalton)
- Subject: AA sequence databases
- 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
bairoch;at;cmu.unige.ch
==============================================================================
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; 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 : Jaime 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 |
| 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; bairoch;at;cmu.unige.ch
Organism : Department of Molecular biology / Massachussetts General Hospital
Address : frodo.mgh.harvard.edu (132.183.190.10)
Databases: EMBL, Codon
Contact : Mike Cherry; cherry;at;frodo.mgh.harvard.edu
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; dbd;at;theory.bchs.uh.edu
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; archive;at;bio.indiana.edu
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; hunter;at;nlm.nih.gov
Organism : Molecular Biology Computer Research Resource (MBCRR)
Address : mbcrr.harvard.edu (134.174.51.4)
Databases: Plsearch
Directory= /MBCRR-Package
Contact : Temple Smith; tsmith;at;mbcrr.harvard.edu
Organism : Human Genome Data Base / Johns Hopkins University
Address : mendel.welch.jhu.edu (128.220.59.42)
Databases: GDB, OMIM.
Contact : GDB User Support; help;at;welch.jhu.edu
Organism : Protein Data Bank (PDB)
Address : pdb.pdb.bnl.gov (130.199.144.1)
Databases: PDB
Contact : skora;at;bnl.gov.
Organism : The Salk Institute for Biological Studies
Address : salk-sc2.sdsc.edu (192.31.153.12)
Databases: PKCDD
Contact : Anne Marie Quinn; quinn;at;salk-sc2.sdsc.edu
Organism : New England BioLabs (NEB)
Address : vent.neb.com (192.138.220.2)
Databases: Rebase
Directory= /pub/rebase
Contact : Dana Macelis; macelis;at;neb.com
Organism : NCI-FCRDC
Address : fconvx.ncifcrf.gov (129.43.52.4)
Databases: GenPept
Directory= /pub/genpept
Contact : Mark A. Gunnell; gunnell;at;ncifcrf.gov
Organism : Pittsburgh Supercomputing Center (PSC)
Address : ftp.psc.edu (128.182.62.148)
Databases: GenBank
Directory= /biomed/genbank/annotated
Contact : Alex Ropelewski; ropelews;at;psc.edu
Organism : BIOSCI at IntelliGenetics
Address : net.bio.net (134.172.2.69)
Databases: BIOSCI documents (including FAQ)
Directory= /pub/BIOSCI
Contact : Dave Kristofferson; kristoff;at;net.bio.net
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; ajb;at;s-crim1-dl.ac.uk
==============================================================================
--
Mark Dalton AUG-GCU-AGA-AAG H
Cray Research, Inc. M A R K |
Eagan, MN 55121 CH3-S-CH2-CH2-C-COOH
Internet: mwd;at;cray.com |
(612)683-3035 NH2