Molecular Biology FTP and Server Sites

Gribskov, Michael gribskov at ov
Sun Dec 16 15:29:00 EST 1990


My thanks to all those who responded to my request for information about 
FTP and servers sites of interest to molecular biologists.  The response 
was considerably greater than I expected and it therefore took some time 
to produce the following list.

I not completely satisfied with this list, but I thought it would be
good to get the current version distributed, and to work on  an improved
version next year.  I think that a more detailed version of the list
would be useful; I would particularly appreciate some feedback on the
level of detail that people would like to see and suggestions on the
most useful format for a more detailed listing.  If you know of other
sites that should be included, or find errors please let me know. 

Michael Gribskov
gribskov at ncifcrf.gov
--------------------------------------------------------------------------------
Molecular Biology FTP and Server List (16 December 1990)

The address for each site is shown in the left column, with the numerical
intenet address below, if it was available.  This is followed by the mail
address of the responsible person, or an address for more information.  For
FTP sites, the directory containing the relevent material is shown in
parentheses if it is other than the default directory.  Note that the larger
FTP sites have a great deal of material of general interest in addition to
what is shown here. 

For bulletin boards, the subscription address is shown in the left 
column, and the address for actual message in parentheses in the center 
column.  

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
		Specific software packages and smaller FTP sites
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
address						contents		
responsible person/more information
+-----------------------------------------------------------------------------
evolution.genetics.washington.edu 	PHYLIP phylogeny package v3.3
128.208.128.1

Joe Felsenstein*, joe at genetics.washington.edu
+-----------------------------------------------------------------------------
anthro.utah.edu.			PHYLIP phylogeny package v3.3
128.110.192.93				(officially sanctioned by author)

Alan Rogers, rogers at anthro.utah.edu
+------------------------------------------------------------------------------
haywire.nmsu.edu			gm (gene modeler) package	
128.123.001.032

Chris Fields*, cfields at nmsu.edu
-------------------------------------------------------------------------------
mcclb0.med.nyu.edu			USENET genbank software			

Ross Smith, smith at mcclb0.med.nyu.edu
+------------------------------------------------------------------------------
ncifcrf.gov       			Delila sequence analysis system 
(/pub/delila)				(150 programs)		

Tom Schneider*, toms at ncifcrf.gov
+------------------------------------------------------------------------------
uvaarpa.virginia.edu  			FASTA database search			
(/public_access/fasta.shar) 		program

William Pearson*, wrp at virginia.edu
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
		Larger FTP sites
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
embl-heidelberg.de 			EMBL
192.54.41.20                            future access to EMBL server
					see netserv at embl entry below
Rainer Fuchs
fuchs at embl.bitnet
+------------------------------------------------------------------------------
flat.nig.ac.jp				DNA Data Bank of Japan
133.39.128.2				Genbank, EMBL, DDBJ
					NBRF, Swissprot, GENPEPT
Sanzo Miyazawa
smiyazaw at nig.ac.jp
+------------------------------------------------------------------------------
genbank.bio.net				Genbank					
134.172.1.160				Genbank database (quarterly)		
(/Public)				Genbank updates (weekly & nightly)
					GenPept db & updates
Dave Kristofferson, 			EMBL db & updates
kristoff at genbank.bio.net 		FASTA searches
consultant at genbank.bio.net		On-line services
					software
-------------------------------------------------------------------------------
iubio.bio.indiana.edu			IUBIO archive	 			
129.79.1.101				Mac,VAX,Atari,DOS software
					LiMB,EPD,TFD,REBASE,DROS
Don Gilbert, 				Prosite
gilbertd at iubio.bio.indiana.edu		Phylip
					Authorin program	
-------------------------------------------------------------------------------
mbcrr.harvard.edu			Molecular Biology Computer 		
134.174.51.4				Research Resource
					software
Temple Smith,				PLSEARCH pattern db 
tsmith at mbcrr.harvard.edu 		MASE 3.1 multiple sequence editor
+------------------------------------------------------------------------------
menudo.uh.edu				U Houston archive
129.7.1.6				Genbank sequence db
					PIR sequence db
Dan Davison, 				UNIX,DOS,VMS,Mac software
dbd at theory.bchs.uh.edu 			Cray software (future)
					BioMatrix archive
					Molecular evolution bb archive
+------------------------------------------------------------------------------
modl.unibas.ch				Biocomputing server			
131.152.1.2				Biozentrum, Universitaet Basel

(/biology/EMBnet)			EMBL ( updated daily)

(/biology/databases)			many databases,e.g.
					alu sequences list
					SwissEnzyme, Prosite
					GCG (3) format codon tables
Reinhard Doelz,				Journal tables of contents
doelz at urz.unibas.ch			LiMB,TFD,ECD,EPD,REBASE,DROS
+------------------------------------------------------------------------------
ncbi.nlm.nih.gov			Natl. Center for Biotech. Information
130.14.20.1				NCBI software
					Geninfo db documentation
Scott Federhen,
federhen at ncbi.nlm.nih.gov		(help and information)

(/repository)				EPD,LiMB,REBASE,SwissENZYME
					metabolism, mol-model

					Transcription factor database (TFD)
					D. Ghosh*, ghosh at ncbi.nlm.nih.gov

(/toolbox)				assorted public domain software
(/pub)					more software - blast, fasta, macaw,etc

(/pub/aimb-db)				AI and molecular biology researchers db
					Lawrence Hunter*, hunter at nlm.nih.gov
+------------------------------------------------------------------------------
nic.funet.fi                            Finnish State Supercomputer Center
128.214.6.100                           Center for Scientific Computing
(pub/misc/molbio)                       VAX, Unix, DOS, Mac software
                                        many non-biological applications
Rob Harper, harper at csc.fi
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
		Server sites
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
bioserve%genome at lanl.gov (2)		Los Alamos National Laboratory server
					Genbank documentation			
Michael Cinofsky,			software archive (future)
michael%domain at lanl.gov	
-------------------------------------------------------------------------------
fileserv at gunbrf.bitnet (2)		PIR server				
					Genbank and GENPEPT

Dr. John S. Garavelli, garavell at gunbrf.bitnet		
Ms. Kathryn Sidman,   pirmail at gunbrf.bitnet
+------------------------------------------------------------------------------
gene-server at bchs.uh.edu (1)		U Houston gene server			
					Genbank sequence db
gene-server-management at bchs.uh.edu	PIR sequence db
					UNIX,DOS,VMS,Mac software
					Cray software (future)
					BioMatrix archive
					Molecular evolution bb archive
					FASTA searches
-------------------------------------------------------------------------------
listserv at irlearn.bitnet (2)		IRLEARN list server			
					BIOSCI newsgroups & archives

					Newsgroups:
					AGEING, AG-FORST, BIO-NAUT, BIONEWS, 
					BIO-JRNL, BIOMATRX, BIO-SOFT, CHROM-22, 
					EMBL-DB, BIOJOBS, GENBANKB, GENE-ORG, 
					ORG, GNOME-PR, METHODS, MOL-EVOL, 
					POP-BIO, PROTEINS, SCI-RES
Rob Harper, harper at csc.fi		(Newsgroup at irlearn.bitnet)		
					e.g. AGEING at irlearn.bitnet
-------------------------------------------------------------------------------
listserv at taunivm.bitnet	(2)		photosynthesis researchers bb		
                                        (photosyn at taunivm.bitnet)	
Jonathan Marder, marder at hujiagri.bitnet
-------------------------------------------------------------------------------
listserv at utoronto.bitnet (2)		U Toronto list server			

John Cargill 				GCG (3) software discussion group
cargill at utoroci.bitnet			(info-gcg at utoronto.bitnet)
cargill at galen.oci.utoronto.ca
+------------------------------------------------------------------------------
netserv at embl.bitnet (2)			EMBL server				
					EMBL (updated daily)
					SwissProt, Prosite
					PDB (Brookhaven db)
					PC, UNIX, Mac & VAX software
					LiMB, ECD, EPD, TFD, SwissEnzyme
					DROS, SEQREF
search at embl.bitnet (2)			FASTA searches
quick at embl.bitnet (2)			Quicksearch (4) searches

Rainer Fuchs, fuchs at embl.bitnet
-------------------------------------------------------------------------------
netserv at flat.nig.ac.jp (2)		FLAT DB E-Mail Network Server

					DDBJ,Genbank(updated 2x daily)
Sanzo Miyazawa				GENPEPT, EMBL(+new entries)
smiyazaw at nig.ac.jp 			SwissProt, PIR, PRF
					keyword searches by author, 
					journal, accession, and description
+------------------------------------------------------------------------------
					Genbank	server				
search at genbank.bio.net (2)		FASTA searches	
retrieve at genbank.bio.net		Sequence retrieval			

genbank at genbank.bio.net
consultant at genbank.bio.net		(help with FASTA)
retrieve-request at genbank.bio.net	(help with retrieval)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
	Anticipated availability: fall of 1991.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Kenneth Kidd, Martin Mador 		Biology Software Info. Clearinghouse
genmlm at yalevm.bitnet			Online software database
					peer reviews
					software archive
					bug reports
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
* indicates that the contact person is the author of the database or program
(1) for information on this server send the message "help" in subject
(2) for information on this server send the message "help" as the first line of 
    the message
(3) Genetics Computer Group Sequence Analysis Package
(4) The GCG (3) program quicksearch with enhancements added at EMBL is
    used to check if a new sequence has been previously sequenced. The
    search is much faster than FASTA, but is will only find nearly identical
    sequences. 

db = database
bb = bulletin board (or discussion group)
DROS     Drosophila clones, maps and genetic deficiencies databases
ECD	 E. coli database
EMBL	 European Molecular Biology Laboratory DNA sequence db
EPD      Eukaryotic Promoter Database (Philip Bucher)
GENPEPT  Genbank translated protein database
LiMB     Listing of Molecular Biology databases (Lawerence Hunter,NCBI)
PIR	 Protein Information Resource (NBRF protein sequence db)
PRF	 Protein Research Foundation db
REBASE   Restriction Enzyme database (Richard Roberts)
SEQREF   SEQANALREF - sequence analysis reference list
TFD      Transcription Factor Database (D.Ghosh,NCBI)




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