FYI

Dr Tan Tin Wee bchtantw at nuscc.nus.sg
Wed Aug 25 10:56:13 CDT 1993


For your information.


    Tin-Wee TAN                        /  INTERNET: bchtantw at nuscc.nus.sg
    Dept of Biochemistry               /  BITNET:   BCHTANTW at NUSVM
    National University of Singapore   /  Tel:      (65)-772-3678
    Singapore 0511                     /  Fax:      (65)-779-1453

---------- Forwarded message ----------
Date: Wed, 25 Aug 93 23:48:48 +0800
From: Gopher Mail Server <mcbserve at nusunix1>
To: bchtantw at nuscc.nus.sg
Subject: MAILGOPHER REPLY - Database of mailgopher sites

Created by T.W.Tan, 24 May 1993; Updated 17;20,21 July 1993
-----------------------------------------------------------------------------

This document may be obtained be sending the message

GOPHERDB

to mcbserve at nusunix2.nus.sg
or mailgopher at nusunix1.nus.sg
or mcbserve at nusunix1.nus.sg

LIST OF USEFUL MAILGOPHER database searches
-------------------------------------------

A list of databases which can be searched using mailgopher is currently
being prepared. This list will be updated on a monthly basis (if our
work schedule permits) and posted on the network.

To carry out a search or retrieval, send email to


      mcbserve at nusunix2.nus.sg (or mcbserve at nusunix1.nus.sg)
OR
      mailgopher at nusunix1.nus.sg

Leave the Subject line blank
Precede the body of the request with the string "GOPHER"
Copy one the following blocks of Host, Port, Path, Type... exactly,
if possible, without trailing spaces, or control characters, etc.
If the entry is a search type=7, add keywords for searching in one line eg.

keyw=keyword1 keyword2 .....

For some gopher sites, boolean searches using "and" and "not" and partial
literals (eg. keyw=Escheri*) are possible; whether they are or not, will
have to be determined by trial and error, because it is not specified.


WARNING:
(Network unreliability and computer down time necessitates redundancy
in the list of sites offering database searches. If results are negative,
it could be the gopher site is down or being maintained.)
biox.embnet.unibas.ch searches were not available when tested on 23 May 1993
(but it should be up by now (17 Jul 1993).
ftp.bchs.uh.edu searches were not available when tested on 23 May 1993
but should be up now (17 Jul 1993).

A. SEQUENCE DATABASES

1. Combined databases

Name=Search GenBank + Swiss-Prot + PIR + PDB (NIH)
Host=gopher.nih.gov
Port=70
Type=7
Path=mindex:/molbio/all.mindex

Name=Search GenBank, PIR, EMBL, and Updates (Houston)
Type=7
Port=195
Path=7/
Host=ftp.bchs.uh.edu


2. DNA sequences

name=Search Genbank release 76 (NIH)
host=gopher.nih.gov
port=70
type=7
path=7/gopherlib/indices/genbank/index

Name=Search Genbank (IUBio)
Host=fly.bio.indiana.edu
Port=70
Type=7
Path=7/.indices/genbank

Name=Search Genbank Updates (IUBio)
Host=fly.bio.indiana.edu
Port=70
Type=7
Path=7/.indices/gbnew

Name=Simultaneous search in all XXEMBL XEMBL EMBL sections
Type=7
Port=13023
Path=1/
Host=biox.embnet.unibas.ch
Note=Discrepancy between path 1/ and type=7?

Name=Search DDBJ, DNA Data Bank of Japan (NIG, Japan)
Type=7
Port=70
Path=waissrc:/DDBJ_Gopher_WAIS/DNA_seq_index_search.src
Host=gopher.nig.ac.jp

3. Protein Sequences

name=Search Swiss-prot Release 25
host=gopher.nih.gov
port=70
type=7
path=7/gopherlib/indices/swiss/index

Name=Fetch PIR entries by accession no.
Type=7
Port=160
Path=
Host=ftp.bchs.uh.edu

Name=Search PIR database by keyword,species,etc
Type=7
Port=160
Path=
Host=ftp.bchs.uh.edu

name=Search PIR Release 35
host=gopher.nih.gov
port=70
type=7
path=7/gopherlib/indices/pir/index

Name=NRL_3D Protein Sequence-Structure Database
Host=merlot.welch.jhu.edu
Port=70
Type=7
Path=7/.INDEX/nrl3d

B. MOLECULAR BIOLOGY DATABASES

Name=Search REBASE, Restriction Enzyme Database
Host=merlot.welch.jhu.edu
Port=70
Type=7
Path=7/.INDEX/rebase

Name=Search TFD, Transcription Factor Database
Host=gopher.nih.gov
Port=70
Type=7
Path=7/gopherlib/indices/tfd/index

Name=Search Cloning Vectors
Host=merlot.welch.jhu.edu
Port=70
Type=7
Path=7/.INDEX/vector

Name=Search EPD, Eukaryotic Promoter Database
Host=merlot.welch.jhu.edu
Port=70
Type=7
Path=7/.INDEX/epd

Name=Search EST, Human Expression Sequence Tags Database
Host=merlot.welch.jhu.edu
Port=70
Type=7
Path=7/.INDEX/est

Name=Search wEST, C.elegans worm Expressed Sequence Tag Database
Host=merlot.welch.jhu.edu
Port=70
Type=7
Path=7/.INDEX/west


C. STRUCTURE DATABASES

Name=Retrieve PDB Protein Databank by Accession Number
Host=merlot.welch.jhu.edu
Port=3000
Type=7
Path=7/

Name=Search PDB headers (Brookhaven)
Host=predator.pdb.bnl.gov
Port=70
Type=7
Path=7/waissrc:/Protein-Data-Bank.src

Name=Search PDB headers (NIH)
Host=gopher.nih.gov
Port=70
Type=7
Path=7/gopherlib/indices/pdb/index


D. BIOCHEMICAL DATABASES

Name=Search ENZYME database
Type=7
Port=163
Path=1/
Host=biox.embnet.unibas.ch
Note=Discrepancy between path 1/ and type=7?

Name=Search EC-ENZYME database
Type=7
Port=70
Path=7/.INDEX/ec-enzyme
Host=merlot.welch.jhu.edu

Name=Search CompoundKB - Metabolic Compounds Database
Type=7
Port=70
Path=waissrc:/Database-Searches/.wais/biology-compounds.src
Host=merlot.welch.jhu.edu

Name=Search PROSITE database
Type=7
Port=164
Path=1/
Host=biox.embnet.unibas.ch
Note=Discrepancy between path 1/ and type=7?

name=Search PROSITE Version 10 December 1992
host=solomon.technet.sg
port=2100
type=7
path=waissrc:/biocomp/BioDatabases/Protein/.index/prosite
keyw=sweet not thaumatin   (example of keywords you can use)

name=Search PROSITE
host=gopher.nih.gov
port=70
type=7
path=7/gopherlib/indices/prosite/index

E. IMMUNOLOGICAL DATABASE

Name=Kabat Database of Proteins of Immunological Interest
Type=7
Port=70
Path=7/.INDEX/kabat
Host=merlot.welch.jhu.edu

F. DISEASE DATABASE

Name=Search OMIM database, Online Mendelian Inheritance in Man
Host=merlot.welch.jhu.edu
Port=70
Type=7
Path=7/waissrc:/Database-local/.wais/OMIM-Online-Mendelian-Inheritance-in-Man.sr
 c

Name=Search OMIM database, Online Mendelian Inheritance in Man
Type=7
Port=70
Path=waissrc:/WAISes/Everything/online-mendelian-inheritance-in-man.src
Host=mudhoney.micro.umn.edu

Name=CancerNet_Files-Search
Type=7
Port=70
Path=waissrc:/CNET/.index/cn.src
Host=gopher.ncc.go.jp



G. REPOSITORIES of BIOMATERIALS

Name=Molecular Probe Data Base search
Type=7
Port=70
Path=waissrc:/interlab/mpdb/Oligos.src
Host=istge.ist.unige.it

Name=B Line Data Base search
Type=7
Port=70
Path=waissrc:/interlab/bldb/B_Lines.src
Host=istge.ist.unige.it

Name=Cell Line Data Base search
Type=7
Port=70
Path=waissrc:/interlab/cldb/Cell_Lines.src
Host=istge.ist.unige.it

Name=CCINFO WDC culture collections database
Type=7
Port=70
Path=waissrc:/databases/CCINFO.src
Host=fragrans.riken.go.jp

Name=STRAINS database - Bacteria (use with CCINFO)
Type=7
Port=70
Path=waissrc:/databases/STRAINS-bact.src
Host=fragrans.riken.go.jp

Name=STRAINS database - Fungi    (use with CCINFO)
Type=7
Port=70
Path=waissrc:/databases/STRAINS-fungi.src
Host=fragrans.riken.go.jp

Name=STRAINS database - Yeasts   (use with CCINFO)
Type=7
Port=70
Path=waissrc:/databases/STRAINS-yeast.src
Host=fragrans.riken.go.jp

Name=Search The Genome of Drosophila - Redbook
Type=7
Port=70
Path=7/.indices/redbook
Host=ftp.bio.indiana.edu

Name=Museum of Paleontology TYPE Specimen Index (Berkeley)
Host=ucmp1.berkeley.edu
Port=70
Type=7
Path=waissrc:/type/.waisindex/index.src

Name=Search C.elegans strain list (CGC)
Host=elegans.cbs.umn.edu
Port=70
Type=7
Path=7bin/cgcstrains.csh

Name=Search GrainGenes database (Cornell)
Host=greengenes.cit.cornell.edu
Port=70
Type=7
Path=7/.GrainGenes.ndx/index

Name=Search the wheat gene catalogue
Type=7
Port=70
Path=7/.GeneCatalog.ndx/index
Host=greengenes.cit.cornell.edu

Name=Search oat pedigrees
Type=7
Port=70
Path=7/.OatPedigrees.ndx/index
Host=greengenes.cit.cornell.edu

Name=Search HDB, Hybridoma Data Bank
Type=7
Port=70
Path=waissrc:/databases/HDB/HDB.src
Host=fragrans.riken.go.jp

H. BIBLIOGRAPHIC DATABASES

Name=Search Seqanalref - Seq. Anal. Bibliographic Ref. Data Bank
Port=70
Host=merlot.welch.jhu.edu
Type=7
Path=7/.INDEX/seqanalref

Name=Search the Bibliography of Theoretical Population Genetics
Port=70
Host=merlot.welch.jhu.edu
Type=7
Path=7/.INDEX/pop-gen.bib

Name=Search the GenTools Bibliography
Port=70
Host=merlot.welch.jhu.edu
Type=7
Path=7/.INDEX/gentools


I. BIOCOMPUTING SOFTWARE ARCHIVES

Name=Search IUBio archive ReadMes, Docs & Help files
Type=7
Port=70
Path=7/.indices/arcdocs
Host=ftp.bio.indiana.edu

J. TAXONOMY DATABASES

Name=Genbank Taxonomy
Host=merlot.welch.jhu.edu
Port=70
Type=7
Path=7/.INDEX/gen-tax

Name=SWISS-PROT Taxonomy
Host=merlot.welch.jhu.edu
Port=70
Type=7
Path=7/.INDEX/swiss-tax


K. LIST OF BIOGOPHERS

name=American Physiological Society
type=1
port=3300
path=1/
host=gopher.uth.tmc.edu

name=Australian National Botanic Gardens
type=1
port=70
path=1/
host=155.187.10.12

name=Base de Dados Tropical (Tropical Data Base), Campinas, Brasil
type=1
port=70
path=1/
host=bdt.ftpt.br

name=Baylor College of Medicine
type=1
port=70
path=1/
host=gopher.bcm.tmc.edu

name=Bedford Institute of Oceanography in Dartmouth
type=1
port=70
path=1/gopher
host=biome.bio.ns.ca

name=BioInformatics at Australian Natl. U.
type=1
port=70
path=1/
host=life.anu.edu.au

name=Biodiversity and Biological Collections at Harvard
type=1
port=70
path=1/
host=huh.harvard.edu

name=Biological Sciences (Student career guide)
type=1
port=70
path=1/servers/guides/Academic Discussion Lists and Interest Groups/Biological
host=watserv2.uwaterloo.ca

name=C. elegans Strains and Alleles @ UTexas
type=1
port=70
path=1/
host=eatworms.swmed.utexas.edu

name=CAMIS (Center for Advanced Medical Informatics at Stanford)
type=1
port=70
path=1/
host=camis.stanford.edu

name=CIESIN Global Change Gopher
type=1
port=70
path=1/
host=gopher.ciesin.org

name=Caenorhabditis Genetics Center (CGC)
type=1
port=70
path=1/
host=elegans.cbs.umn.edu

name=Chlamydomonas Genetics Center at Duke U.
type=1
port=70
path=1/
host=gopher.duke.edu
or host=atlas.acpub.duke.edu

name=Computational Biology at Johns Hopkins U.
type=1
port=70
path=1/
host=merlot.welch.jhu.edu

name=Cooperative Human Linkage Center (CHLC)
type=1
port=70
path=1/
host=haldane.fccc.edu

name=DNA Data Bank of Japan, Natl. Inst.  of Genetics, Mishima
type=1
port=70
path=1/
host=gopher.nig.ac.jp

name=EMBnet Bioinformation Resource (BIOFTP Switzerland)
type=1
port=70
path=1/
host=bioftp.unibas.ch
or host=biox.embnet.unibas.ch

name=EMBnet Bioinformation Resource (BioBox Finland)
type=1
port=70
path=1/.BioBox
host=finsun.csc.fi

name=EMBnet BioInformation Resource (EMBL Germany)
type=1
port=70
path=1/
host=ftp.embl-heidelberg.de
or host=felix.embl-heidelberg.de

name=EMBnet Bioinformation Resource (France)
type=1
port=70
path=1/
host=coli.polytechnique.fr

name=EMBnet Bioinformation Resource (CAOS-CAMM Center, Netherlands)
type=1
port=70
path=1/
host=camms1.caos.kun.nl

name=EMBnet Bioinformation Resource (INN, Weizmann Institute of Science, Israel)
type=1
port=70
path=1/
host=sunbcd.weizmann.ac.il

name=EMBnet Bioinformation Resource (Spain)
type=1
port=70
path=1/
host=gopher.cnb.uam.es

name=EMBnet Bioinformation Resource (SEQNET UK)
type=1
port=70
path=1/
host=s-crim1.daresbury.ac.uk
or host=s-crim1.dl.ac.uk

name=Ecogopher at the University of Virginia
type=1
port=70
path=1/
host=ecosys.drdr.virginia.edu

name=Ecology and Evolution
type=1
port=70
path=1/../.pub/academic/biology/ecology+evolution
host=sunsite.unc.edu

name=EnviroGopher (CMU)
type=1
port=70
path=1/
host=envirolink.hss.cmu.edu

name=Environmental Resources Information Network (ERIN)
type=1
port=70
path=1/
host=kaos.erin.gov.au

name=FTP-Archives
type=1
port=70
path=1/Other-Bio-Gophers/FTP-Archives
host=ftp.bio.indiana.edu

name=Forestry & Ecological Data Exchange at Yale
type=1
port=70
path=1/Enterprise/Academic/Forestry
host=gopher.yale.edu

name=Forestry Library at U. Minnesota
type=1
port=70
path=1/
host=minerva.forestry.umn.edu

name=GRIN, National Genetic Resources Program, USDA-ARS
type=1
port=70
path=1/
host=gopher.ars-grin.gov

name=Genethon (CEPHB Human Polymorphism Study Center, Paris, France)
type=1
port=70
path=1/
host=gopher.genethon.fr

name=Human Genome Mapping Project Gopher Service (UK)
type=1
port=70
path=1/
host=menu.crc.ac.uk

name=ICGEBnet Int.Center Genet.Engineering & Biotec (Trieste)
type=1
port=70
path=1/
host=genes.icgeb.trieste.it

name=IUBio Biology Archive, Indiana University (experimental)
type=1
port=70
path=1/
host=ftp.bio.indiana.edu

name=Long-Term Ecological Research Network (LTERnet)
type=1
port=70
path=1/
host=lternet.edu

name=MegaGopher at U. Montreal, CA
type=1
port=70
path=1/
host=megasun.bch.umontreal.ca

name=Microbial Germplasm Database at OSU
type=1
port=70
path=1/
host=gopher.bcc.orst.edu

name=Molbio databases at Welchlab, JHU
type=1
port=70
path=1/Database-local
host=merlot.welch.jhu.edu

name=Museum of Paleontology Gopher @ Berkeley
type=1
port=70
path=1/
host=ucmp1.berkeley.edu

name=MycDB (experimental) (France)
type=1
port=70
path=1/
host=arabidopsis.pasteur.fr

name=National Cancer Center, Tokyo JAPAN
type=1
port=70
path=1/
host=gopher.ncc.go.jp

name=National Center for Biotechnology Information (NCBI) Gopher
type=1
port=70
path=1/
host=ncbi.nlm.nih.gov

name=National Institute Allergy & Infectious Disease (NIAID)
type=1
port=70
path=1/
host=gopher.niaid.nih.gov

name=National Institute for Cancer Research (IST, Genova, Italy)
type=1
path=1/
port=70
host=istge.ist.unige.it

name=National Institutes of Health (NIH) Gopher
type=1
port=70
path=1/
host=gopher.nih.gov

name=National Science Foundation Gopher
type=1
port=70
path=1/
host=stis.nsf.gov

name=National University of Singapore
type=1
port=70
path=1/BioComputing
host=solomon.technet.sg

name=Nucleic Acid Database - NDB (Rutgers)
type=1
port=17105
path=1/
host=ndb.rutgers.edu

name=PIR Archive, University of Houston
type=1
port=70
path=1/
host=ftp.bchs.uh.edu

name=Plant Genes: Arabidopsis AAtDB Server
type=1
port=70
path=1/
host=weeds.mgh.harvard.edu

name=Plant Genes: Dendrome Genome Database (Institute of Forest Genetics)
type=1
port=70
path=1/
host=s27w007.pswfs.gov

name=Plant Genes: GrainGenes, the Triticeae Genome Gopher
type=1
port=70
path=1/
host=greengenes.cit.cornell.edu

name=Plant Genes: Maize Genome Database
type=1
port=70
path=1/
host=teosinte.agron.missouri.edu

name=Plant Genes: National Agricultural Library Plant Genome
type=1
port=70
path=1/
host=locus.nalusda.gov

name=Plant Genes: Soybean Data (SoyBase)
type=1
port=70
path=1/
host=mendel.agron.iastate.edu

name=Primate Information Network
type=1
port=70
path=1/
host=uakari.primate.wisc.edu

name=Protein Data Bank ftp Site
type=1
port=70
path=1/
host=pdb.pdb.bnl.gov

name=SEQNET EMBNet UK
type=1
port=70
path=1/
host=148.79.64.2

name=U. Georgia Botany Department
type=1
port=70
path=1/
host=dogwood.botany.uga.edu

name=U. Georgia Ecology Department
type=1
port=70
path=1/
host=sparc.ecology.uga.edu

name=U. Georgia Zoology Department
type=1
port=70
path=1/
host=zookeeper.zoo.uga.edu

name=U. Western Australia Virology Gopher
type=1
port=70
path=1/
host=virus.microbiol.uwa.edu.au

name=USDA Extension Service
type=1
port=70
path=1/
host=ra.esusda.gov

name=University of Wisconsin Biotechnology Center
type=1
port=70
path=1/
host=calvin.biotech.wisc.edu

name=University of Wisconsin-Madison, Medical School
type=1
port=70
path=1/
host=msd.medsch.wisc.edu

name=Various Electronic Serials for Science (CIC)
type=1
port=70
path=1/e-serials/Science
host=gopher.cic.net

name=Wide-Area-Info-Servers
type=1
port=70
path=1/Other-Bio-Gophers/Wide-Area-Info-Servers
host=ftp.bio.indiana.edu

name=World Data Center on Microorganisms (WDC), RIKEN, Japan
type=1
port=70
path=1/
host=fragrans.riken.go.jp


L. SPECIES DATABASES

Name=Flybase - Drosophila Database
Type=1
Port=70
Path=1/Flybase
Host=ftp.bio.indiana.edu

Name=MycDB - Mycobacterium Database
Host=arabidopsis.pasteur.fr
Port=70
Type=7
Path=7/.mycdb/.waisindex/index

Name=Search AAtDB - An Arabidopsis thaliana Database
Host=weeds.mgh.harvard.edu
Port=70
Type=7
Path=7/.index/Arabidopsis_thaliana_Genome

Name=Search ACEDB - A Caenorhabditis elegans Database
Host=weeds.mgh.harvard.edu
Port=70
Type=7
Path=7/.index/Caenorhabditis_elegans_Genome





M. EMAIL DISCUSSION GROUPS ARCHIVES

Name=Search for Bionet News at IUBio archive
Type=7
Port=70
Path=7/.indices/netnews
Host=ftp.bio.indiana.edu



N. DATABASE OF DATABASES

Name=Search LiMB, Listing of Molecular Biology Databases
Type=7
Port=70
Host=gopher.nih.gov
Path=7/gopherlib/indices/limb/index

Name=Search for a line in the biogopher trees (not ready)
Type=0
Port=70
Path=0/biogopher_trees/search for a line in the gopher trees <?>
Host=yeti.embnet.unibas.ch


IMPORTANT NOTES:
Many of these Gopher databases are created and maintained voluntarily by
maintainers throughout the world and are subject to change without
warning. If you have difficulty getting something back, try mailgopher
to the root directory of the host first, eg. use type=1 and path=1/
(try the default port 70) and slowly work your way down the directory path.

This list presupposes that the user already knows about the database.
If not, try mailgopher to the root directory of the host as described
above and you should find information describing the database available for
retrieval.




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