The ExPASy Molecular Biology Server
List of documents concerning molecular biology oriented
services, software, email servers, FTP sites, etc.
Name : listdoc.txt
Version: 3.41 / October 13, 1995
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@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 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 organizations
serv_ftp .txt List of molecular biology FTP servers for databases and software
serv_ema .txt List of molecular biology email servers
serv_bbo .txt List of bulletin boards services for molecular biologists
atcc .txt Internet access to catalog data at ATCC
biobit25 .txt Bio-Naut newsletter 25-1-95
biosci_e .txt BIOSCI electronic newsgroup network (European info sheet)
biosci_u .txt BIOSCI electronic newsgroup network (US/Pacific info sheet)
biotechn .txt BioTechNET; global computer network for research biologists
ebi .txt European Bioinformatics Institute (EBI) press releases
embnet1 .txt EMBnet: European Molecular Biology Data Network (1990)
embnet2 .txt The nodes of EMBnet by R. Doelz (Release 0.9 of fall 1993)
embnet92 .txt Article about the EMBnet Project by R. Doelz
embnet_f .txt Status of the French EMBnet node (September 1994)
embnnews .txt Information about the EMBnet News newsletter
faq_bio .txt Frequently Asked Questions (FAQs) about BIOSCI/bionet
faq_meth .txt Frequently Asked Questions for bionet.molbio.methds-reagnts
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 databases
biocatal .dba BioCatalog
buaddres .dba BIOSCI User Address Database
cpgisle .dba CpG Islands Database
dbest .dba dbEST - a public database of "expressed sequence tags"
ddbj .dba Brief Outline of DDBJ (DNA Data Bank of Japan)
ecocyc .dba EcoCyc; the encyclopedia of E. coli genes and metabolism
embl .dba EMBL Data Library Products and Services
gcrdb .dba GCRDb (G Protein Coupled Receptor database)
gdbomim .dba GDB (Genome d.b.) & OMIM (Online Mendelian Inheritance in Man)
genbank .dba List of GenBank services
hybridom .dba Hybridoma Data Bank (HDB)
hovergen .dba Homologous Vertebrate Genes Data Base
imgt .dba ImMunoGeneTics database (IMGT)
nrsub .dba NRSub (Non-Redundant Bacillus subtilis) database
omega .dba OMEGA data bank
subtilis .dba SubtiList database
tmbase .dba TMbase - database of transmembrane domains
transfac .dba TRANSFAC database
Documents describing email servers
bicserv .srv Bicserv [Similarity searches]
biosafet .srv Biosafety [Retrieval of biosafety documents]
bioscan .srv BioSCAN [Similarity searches]
bioserve .srv BIOSERVE [Retrieval of various documents and software]
blast .srv NCBI BLAST [Similarity searches]
blitz .srv EBI 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]
domain .srv DOMAIN [Domain oriented sim. search against SW-PROT]
estmail .srv NCBI EST [Retrieval of Expressed sequence tag sequences]
fastamai .srv EBI FASTA [Similarity searches]
flatserv .srv Flat DB [Retrieval of sequences from databases]
gcrdb .srv GCRDb [Similarity search against GCRDb]
gdbomim .srv GDB/OMIM [Retrieval of GDB and OMIM data]
geneid .srv Geneid [Protein coding region prediction]
genefind .srv Genefinder [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]
hugemap .srv HUGEMAP [Retrieval of human physical map data]
motifind .srv MotifFinder [Prosite]
mowse .srv MOWSE [Peptide mass fingerprint]
netgene .srv NetGene [Protein coding region prediction]
netserv .srv EBI 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]
prodom .srv ProDom [Protein domains]
prosite .srv Prosite [Prosite]
psort .srv PSORT [Predict protein sorting signals & localizat.]
pythia .srv Pythia [Identification of repetitive DNA elements]
quickmai .srv EBI 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]
signalp .srv signalp [Signal peptides detection]
sopm .srv SOPM [Protein secondary structure prediction]
springer .srv Springer [Retrieval of table of contents of journals]
tmap .srv TMAP [Protein transmembrane segments prediction]
tm7 .srv TM7 [Retrieval of data on G protein-coupled recep.]
waismail .srv WaisMail [Retrieval of BIOSCI postings and other doc.]
ypd .srv YPD [Retrieval of data from yeast protein database]
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
able .sof ABLE; test for constancy in the evolutionary rates
anthepro .sof ANTHEPROT; protein analysis software package
bandlead .sof Band Leader; Gel images processing software
biosim .sof BIOSIM; biologically oriented neural network simulator
blast .sof BLAST; Basic Local Alignment Search Tool version 1.4
boxshade .sof BOXSHADE; creates nice printouts from multiple-alignments
chrozoom .sof ChromoZooM; tool for comparison and alignment of images
clever .sof Clever; COmmand Line Entrez VERsion
colibri .sof Colibri; Macintosh E.coli genome data base application
cost .sof Cost; a fast random cost algorithm for physical mapping
degendes .sof DegenDesigner; design degenerate oligos (for PCR or blotting)
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.
falcon .sof FALCON; Fast Assembly of Large CONtigs
fastaler .sof FastAlert; FastA Best Scores Alerting System
foldit .sof Foldit (light); Mac protein molecular modelling program
gbsoft .sof GenBank Software Clearinghouse
gdb_lite .sof GDB-Lite; browsing and data entry tool for the Genome Data Base
gdb_acce .sof GDB/Accessor; MacIntosh program for accessing GDB on Internet
hmmer .sof HMMER; Hidden Markov models for protein & n.a sequence analysis
icatools .sof ICAtools; clustering and database searching programs
macblast .sof Macintosh BLAST Client
mega .sof MEGA; Molecular Evolutionary Genetics Analysis
memsat .sof MEMSAT; transmembrane structure prediction program
mitoprot .sof MitoProt; evaluation of mitochondrial targeting sequences
msblast .sof MSBLAST; Multible Sequence Blast
namot .sof NAMOT; Nucleic Acid Modeling Tool
ncbitool .sof NCBI ASN.1 software toolkit
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
pdbcat .sof PDBCAT; converts PDB files to a field based format & back again
phylogen .sof Some available phylogeny programs
proanal .sof ProAnal; analysis of relationship between structure/activity
prophet .sof Prophet; UNIX-workstation software package
prosa .sof PROSA II; PROtein Structure Analysis
rasmol .sof RasMol; Molecular Graphics Visualisation tool
rnadraw .sof RNAdraw; RNA secondary structure/Basepair probability software
scanps .sof SCAPS; Protein sequence similarity scanning program
seqpup .sof SeqPup; Biological sequence editor and analysis program
sigma .sof SIGMA; System for Integrated Genome Map Assembly
smite .sof SMITE; query language for the PRINTS protein fingerprint db
threader .sof THREADER; protein 3D structure threading software
treecon .sof TREECON; construction and drawing of evolutionary trees
wordup .sof WORDUP; Dynamic detection of signals in a DNA sequence
wpdb .sof WPDB; Windows based Macromolecular Structure Interrogation
Miscellanous
gerotoge .txt Articles on gerontogenes (FASEB J. 9:284-286(1995).
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@cmu.unige.ch
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