MAILGOPHER list of databases (Large!)

[Gopher Mail Server]

To accompany the earlier post announcing the MAILGOPHER experimental
email server at the National University of Singapore, the following
is posted for the convenience of users.

This list is certainly not exhaustive, and we would appreciate it if
BioGopher maintainers email us with your latest updates
(bchtantw at nuscc.nus.sg)

There are probably many errors, and I hope users who detect them will
kindly bear with me and inform me so that I can get them straightened out.

Thank you.

Tin Wee
bchtantw at nuscc.nus.sg








Created by T.W.Tan, 24 May 1993
-----------------------------------------------------------------------------

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 mailgopher at nusunix2.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.

Your reply should come back very quickly and certainly not more than a day
(unless we are completely swamped, or our internet line is down). Search
hits will come back in a similar format as that below.

WARNING:
(Network unrealiability 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.) For example:
biox.embnet.unibas.ch searches were not available when tested on 23 May 1993.
ftp.bchs.uh.edu searches were not available when tested on 23 May 1993.
merlot.welch.jhu.edu gopher appears down when connection tested from nuscc.nus.sg

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.src

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

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 DataBase
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

Could maintainers send me a list of their own gophers and "Other-BioGophers"
please?

L. SPECIES DATABASES

Name=Flybase
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.