List of documents available on expasy

Amos Bairoch BAIROCH at cmu.unige.ch
Thu Feb 10 19:05:21 EST 1994


==============================================================================
Name   : listdoc.txt
Version: 1.00 / February 3, 1994
Concern: List of documents concerning molecular biology oriented services,
         software, email servers, FTP sites, etc.
Author : Amos Bairoch / Dept. Medical Biochemistry
         University of Geneva / Switzerland
         Email to: bairoch at cmu.unige.ch
==============================================================================

All the documents listed below are available:

- By anonymous FTP from: expasy.hcuge.ch  (129.195.254.61)
                         In the directory: /databases/info

- By the World-Wide Web (WWW) from the ExPASy molecular biology server
  The URL for the ExPASy is: http://expasy.hcuge.ch/

- On the PC/Gene data banks CD-ROM disk 2 in the directory: \OTHERS\INFO

---------------------------------------------------------------------------
General information documents or documents describing specific orgnizations
---------------------------------------------------------------------------

serv_ema .txt  List of molecular biology email servers
serv_ftp .txt  List of molecular biology FTP servers for databases and software
serv_bbo .txt  List of bulletin boards services for molecular biologists
          
atcc     .txt  Internet access to catalog data at ATCC
biosci   .txt  BIOSCI electronic newsgroup network
biotechn .txt  BioTechNET; global computer network for research biologists
bisance  .txt  BISANCE, French service for access to biomolecular sequence d.b.
ddbj     .txt  Brief Outline of DDBJ (DNA Data Bank of Japan)
ebi      .txt  The European Bioinformatics Institute (EBI)
embl     .txt  EMBL Data Library Products and Services
embnet   .txt  EMBnet: European Molecular Biology Data Network
embnet92 .txt  Article about the EMBnet Project by R. Doelz
faq_bio  .txt  Frequently Asked Questions (FAQs) about BIOSCI/bionet
faq_meth .txt  Frequently Asked Questions for bionet.molbio.methds-reagnts
gdbomim  .txt  GDB (Genome D.B.) & OMIM (Online Mendelian Inheritance in Man)
genbank  .txt  List of GenBank services
hovergen .txt  Homologous Vertebrate Genes Data Base
icgeb    .txt  Int. Centre for Genetic Engineering and Biotechnology (ICGEB)
ig_prod  .txt  Summary of IntelliGenetics software and services
interbio .txt  Una Smith Biologist's Guide to Internet Resources
msdn     .txt  Services provided by the Microbial Strain Data Network (MSDN)
ncbi     .txt  Goals of the National Center for Biotechnology Informat. (NCBI)
nir      .txt  Network information retrieval (NIR), a summary
yeast_em .txt  Yeast researchers Email address list

----------------------------------
Documents describing email servers
----------------------------------

bioscan  .srv  BioSCAN         [Similarity searches]
bioserve .srv  BIOSERVE        [Retrieval of various documents and software]
blast    .srv  NCBI BLAST      [Similarity searches]
blitz    .srv  EMBL BLITZ      [Similarity searches]
blocks   .srv  BLOCKS          [Similarity searches against BLOCK; retrieval]
dapmail  .srv  DAPMAIL         [Similarity searches]
darwin   .srv  Darwin          [Various analytical functions]
dflash   .srv  dFLASH          [Similarity searches]
estmail  .srv  NCBI EST        [Retrieval of Expressed sequence tag sequences]
fastamai .srv  EMBL FASTA      [Similarity searches]
flatserv .srv  Flat DB         [Retrieval of sequences from databases]
gdbomim  .srv  GDB/OMIM        [Retrieval of GDB and OMIM data]
geneid   .srv  Geneid          [Protein coding region prediction]
genmark  .srv  GenMark         [Protein coding region prediction]
genquest .srv  GenQuest        [Similarity searches]
grail    .srv  Grail           [Protein coding region prediction]
houston  .srv  Gene-Server     [Retrieval of sequences and software]
mowse    .srv  MOWSE           [Peptide mass fingerprint]
netgene  .srv  NetGene         [Protein coding region prediction]
netserv  .srv  EMBL NetServ    [Retrieval of software, doc  and databases]
nnpredic .srv  nnpredict       [Protein secondary structure prediction]
pir      .srv  PIR             [Retrieval of sequences & similarity searches]
predprot .srv  PredictProtein  [Protein secondary structure prediction]
pythia   .srv  Pyhia           [Identification of repetitive DNA elements]
quickmai .srv  QUICKSEARCH     [Similarity searches]
rdp      .srv  RDP             [Retrieval of data/soft. from Rib. Db. Project]
retrieve .srv  NCBI RETRIEVE   [Retrieval of sequences from databases]
sbase    .srv  SBASE           [Similarity searches against SBASE]
springer .srv  Springer        [Retrieval of table of contents of journals]
tm7      .srv  TM7             [Retrieval of data on G protein-coupled recep.]
waismail .srv  WaisMail        [Retrieval of BIOSCI postings and other doc.]


--------------------------------
Documents describing FTP servers
--------------------------------

gdbnetjp .ftp  Genome Database Network in Japan (GDBnetJP) FTP server
gdbomim  .ftp  How to access GDB & OMIM files via FTP
iubio    .ftp  IUBIO FTP archive
pdb      .ftp  Protein Data Bank via FTP
suhgmc   .ftp  Stanford University human genome mapping center FTP server

--------------------------------------
Documents describing software packages
--------------------------------------

anthepro .sof  ANTHEPROT; protein analysis software package
biosim   .sof  BIOSIM; biologically oriented neural network simulator
blaze    .sof  BLAZE, massively parallel sequence similarity search program
clever   .sof  Clever: COmmand Line Entrez VERsion
detect   .sof  DETECT; a program that locates errors in DNA sequences
dnawkbn  .sof  DNA WorkBench; a program for sequence searching and manipulation
dsce     .sof  DCSE, multiple sequence alignment editor (DOS,VMS,IRIX)
egcg     .sof  EGCG; package of 65 programs which extend the GCG package
emblsoft .sof  List of DOS, Mac, Unix, VAX soft. available from EMBL file serv.
gbsoft   .sof  GenBank Software Clearinghouse
gdb_lite .sof  GDB-Lite; browsing and data entry tool for the Genome Data Base
icatools .sof  ICAtools; clustering and database searching programs
mega     .sof  MEGA: Molecular Evolutionary Genetics Analysis
ods      .sof  ODS; Ordering DNA Sequences ("contig mapping")
oxford   .sof  University of Oxford software packages (alscript, amps, etc.)
pcap     .sof  PCAP; probe choice and analysis package
phylogen .sof  Some available phylogeny programs
proanal  .sof  ProAnal; analysis of relationship between structure/activity

==============================================================================

-------
CAVEATS
-------

- Except for the serv_ftp.txt, serv_ema.txt and serv_bbo.txt documents, we are
  not responsible for the content of these documents.

- We try to  regularily  update  these  documents by  accessing  recent copies
  from the orginal providers,  but  we  can  not insure that we store the most
  recent version.

- If you have a document that you wish to be added  to  this list, please send
  it to my email address (this is also valid for updates/comments):

                  bairoch at cmu.unige.ch



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