Genomics: The Science and Technology Behind the Human Genome Project. |
Charles R. Cantor, Cassandra L. Smith |
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Copyright © 1999 John Wiley & Sons, Inc. |
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ISBNs: 0-471-59908-5 (Hardback); 0-471-22056-6 (Electronic) |
APPENDIX
Databases
GenBank: A public database built and distributed by the National Center for Biotechnology Information.
http://www.ncbi.nlm.nih.gov/
ftp:ncbi.nlm.nih.gov
EMBL Nucleotide Sequence Database: A central activity of the European Bioinformatics Institute; an EMBL outstation.
http://www.ebi.ac.uk
ftp:ftp.ebi.ac.uk
DNA Data Bank of Japan (DDBJ): Activities began in earnest in 1986 in collaboration with EMBL and GenBank.
http://www.ddbj.nig.ac.jp/
ftp:ftp2.ddbj.nig.ac.jp
Genome Sequence DataBase (GSDB): Designed to meet the community-wide challenges of managing, interpreting, and using DNA sequence data at an ever increasing rate.
http://www.ncgr.org/gsdb
Protein Information Resource (PIR) and the PIR-International Protein Sequence Database:
http://www.nbrf.georgetown.edu
ftp:nbrf.georgetown.edu
MIPS: A database for protein sequences, homology data, and yeast genome information:
www.mips.embnet.org
SWISS-PROT protein sequence data bank and its supplement TrEMBL:
www.nlm.nih.gov (or EBI server)
Metabolic pathway collection:
www.cme.msu.edu/WIT/
NRSub database: ftp://biom3.univlyon1.fr/pub/nrsub ftp://ftp.nig.ac.jp/pub/db/nrsub
GDB Human Genome Database: http://gdbwww.gdb.org/ ftp://ftp.gdb.org/
Radiation Hybrid Database: http://www.ebi.ac.uk/RHdb ftp://ftp.ebi.ac.uk/pub/databases/RHdb
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Mouse Genome Database (MGD): A comprehensive public resource of genetic, phenotypic, and genomic data.
ftp://www.informatics.jax.org/
ftp://ftp.informatics.jax.org/pub/
Molecular Probe Data Base (MPDB):
http://www.biotech.ist.unige.it/interlab/mpdb.html
Signal Recognition Particle Database (SPRDB): http://pegasus.uthct.edu/SRPDB/SRPDB.html ftp://diana.uthct.edu
Viroid and viroid-like sequence database: Addition of a hepatitis delta virus RNA section:
http://www.callisto.si.usherb.ca/
Mutation spectra database for bacterial and mammalian genes:
http://info.med.yale.edu/mutbase/
PRINTS protein fingerprint database: http://www.biochem.ucl.ac.uk/bsm/dbbrowser/ ftp://s-ind2.dl.ac.uk/pub/database/prints
PROSITE datases: http://expasy.hcuge.ch/ ftp.ebi.ac.uk
Blocks Database servers: http://blocks.fhcrc.org/ ftp://ncbi.nlm.nih.gov/repository/blocks
HSSP database of protein structure-sequence alignments: http://www.sander.embl-heidelberg.de/ ftp://ftp.embl-ebi.ac.uk/pub/databases/
Dali/FSSP classification of the three-dimensional protein folds: http://www.embl-heidelberg.de/dali/fssp/
DEF database of protein fold class predictions:
http://zeus.cs.uoi.gr/neural/biocomputing/def.html
SCOP: A structural classification of proteins database:
http://scop.mrc-lmb.cam.ac.uk/scop/
SBASE protein domain library: A collection of annotated protein sequence segments:
http://www.icgeb.triester.it http://base.icgeb.triester.it/sbase/(using BLAST)
Codon usage tabulated from the international DNA sequence databases: ftp://ftp.nig.ac.jp/pub/db/codon/current/
TransTerm: translational signal database:
http://biochem.otago.ac.nz:800/Transterm/homepage.html
REBASE: restriction enzymes and methylases:
http://www.neb.com/rebase
Ribonuclease P database:
http://www.mbio.ncsu.edu/RNaseP/home.html
APPENDIX 571
TRANSFAC, TRRD, and COMPEL: Toward a federated database system on transcriptional regulation:
http://transfac.gbf-braunschweig.de http://www.bionet.nsc.ru/TRRD
MHCPER: A database of MHC-binding peptides: http://wehih.wehi.edu.au/mhcpep/ ftp.wehi.edu.au/pub/biology/mhcpep/
Histone and histone fold sequences and structures:
http://www.ncbi.nlm.nih.gov/Basevani/HISTONES/
Directory of P450-containing Systems:
http://www.icgeb.trieste.it/p450
http://p450.abc.hu
O-GLYCBASE: A revised database of O-glycosylated proteins: http://www.cbs.dtu.dk/databases/OGLYCBASE/ ftp.cbs.dtu.dk/pub/Oglyc/Oglyc.base
Mitochondria
MITOMAP: Human mitochondrial genome database:
http://www.gen.emory.edu/mitomap.html
MmtDB: A Metazoa mitochondrial DNA variants database:
http://www.ba.cnr.it/ areamt08/MmtDBWWW.htm
IMGT: International ImMunoGeneTics database:
http://imgt.cnusc.fr:8104
SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis:
http://expasy.hcuge.ch/
GRBase: A database linking information on proteins involved in gene regulation: http://www.access.digex.net/ regulate ftp://ftp.trevigen.com/pub/Tfactors
ENZYME data bank:
http://expasy.hcuge.ch/
E. coli |
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Compilation of DNA sequences of |
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E. coli |
K12: Description of the interactive |
databases ECD and ECDC: |
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http://susi.bio.uni-giessen.de/usr/local/www/html/ecdc.html |
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EcoCyc: Encyclopedia of |
E. coli |
Genes and Metabolism: |
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http://www.ai.sri.com/ecocyc/ecocyc.html |
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GenProtEC: Genes and proteins of |
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E. coli |
K12: |
http://www.mbl.edu/html/ecoli.html |
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Yeast
Yeast Protein Database(YPD): A database for the complete proteome of
Saccharomyces cerevisiae:
http://www.proteome.com/YPDhome.html
LISTA, LISTA-HOP, and LISTA-HON: A comprehensive compilation of protein encoding sequences and its associated homology databases from the yeast
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Saccharomyces:
http://www.ch.embnet.org/
ftp://bioftp.unibas.ch
Drosophila |
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FlyBase: A |
Drosophila |
database: |
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http://flybase.bio.indiana.edu |
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ftp:flybase.bio.indiana.edu(in /flybase) |
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GIF-DB: A WWW database on gene interactions involved in |
Drosophila |
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melanogaster |
development: |
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http://www-biol.univ-mrs.fr/ |
lgpd/GIFTS_home_page.html |
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RNA
Compilation of 5S rRNA and 5S rRNA gene sequences: http://rose.man.poznan.pl/5SData/5SRNA.html http://www.chemie.fu-berlin.de/fb_chemie/ibc/agerdmann/5S_rRNA.html ftp.fu-berlin.de/science/biochem/db/5SrRNA
Small RNA database:
http://mbcr.bcm.tmc.edu/smallRNA/smallrna.html
uRNA database: http://pegasus.uthct.edu/uRNADB/uRNADB.html
guide RNA database: |
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http://www.biochem.mpg.de/ |
goeringe/ |
Ribosomal Database Project (RDP): |
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http://rdpwww.life.uiuc.edu/ |
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ftp://rdp.life.uiuc.edu |
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Database on the structure of small ribosomal subunit RNA:
http://rrna.uia.ac.be/ssu/
Database on the structure of large ribosomal subunit RNA:
http://rrna.uia.ac.be/lsu/
RNA modification database: http://www-medlib.med.utah.edu/RNAmods/RNAmods.html ftp://medlib.med.utah.edu/library/RNAmods
Expansion of the 16S and 23S ribosomal RNA mutation databases (16SMDB and 23SMDB):
http://www.fandm.edu/Departments/Biology/Databases/RNA.html
Compilation of tRNA sequences and sequences of tRNA genes: ftp.ebi.ac.uk/pub/databases/tRNA
Specific gene Haemophilia:
Factor VIII Mutation Database on the WWW: The Haemophilia A Mutation, Search, Test, and Resource Site:
http://europium.mrc.rpms.ac.uk
ftp.ebi.ac.uk/pub/databases/hamsters
Haemophilia B: Database of point mutations and short additions and deletions:
http://www.umds.ac.uk/molgen/haemBdatabase
Database and software for the analysis of mutations in the human
human hpr t gene, and both the lacI, and lacZ gene in transgenic rodents: http://sunsite.unc.edu/dnam/mainpage.html
p53and APC gene mutations: Software and databases
Database of p53gene somatic mutations in human tumors and cell lines: http://www.ebi.ac.uk/srs/
Human
PAH mutation analysis consortium databases:
http://www.cf.ac.uk/uwcm/mg/hgmd0.html
alpha/beta fold family of proteins database and the cholinesterase gene server ESTHER:
http://www.ensam.inra.fr/cholinesterase
Marfan Database: Software and database for the analysis of mutations in the human FBN1 gene
BTKbase, mutation database for X-linked agammaglobulinemia (XLA):
http://www.helsinki.fi/science/signal/btkbase.html
Human type I collagen mutation database:
http://www.le.ac.uk/depts/ge/collagen/collagen.html
Receptors
Androgen receptor gene mutations database: http://www.mcgill.ca/andogendb/ ftp.ebi.ac.uk/pub/databases/androgen
Nuclear Receptor Resource Project:
http://nrr.georgetown.edu/nrr.html
Glucocorticoid receptor resource:
http://biochem1.basic-sci.georgetown.edu/grr/grr.html
APPENDIX 573
p53gene, the