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Table 1. Molecular Biology Database Collection
Major Sequence Repositories
DNA Data Bank of Japan (DDBJ) http://www.ddbj.nig.ac.jp All known nucleotide and protein sequences; International Nucleotide Sequence Database Collaboration
EMBL Nucleotide Sequence Database http://www.ebi.ac.uk/embl.html All known nucleotide and protein sequences; International Nucleotide Sequence Database Collaboration
GenBank http://www.ncbi.nlm.nih.gov/ All known nucleotide and protein sequences; International Nucleotide Sequence Database Collaboration
Genome Sequence Database (GSDB) http://www.ncgr.org/research/sequence/ All known nucleotide and protein sequences
STACK http://www.sanbi.ac.za/Dbases.html Non-redundant, gene-oriented clusters
TIGR Gene Indices http://www.tigr.org/tdb/index.html Non-redundant, gene-oriented clusters
UniGene http://www.ncbi.nlm.nih.gov/UniGene/ Non-redundant, gene-oriented clusters
Comparative Genomics
Clusters of Orthologous Groups (COG) http://www.ncbi.nlm.nih.gov/COG/ Phylogenetic classification of proteins from 21 complete genomes
XREFdb http://www.ncbi.nlm.nih.gov/XREFdb/ Cross-referencing of model organism genetics with mammalian phenotypes
Gene Expression
ASDB http://cbcg.nersc.gov/asdb Protein products and expression patterns of alternatively-spliced genes
Axeldb http://www.dkfz-heidelberg.de/abt0135/axeldb.htm Gene expression in Xenopus
BodyMap http://bodymap.ims.u-tokyo.ac.jp/ Human and mouse gene expression data
EpoDB http://www.cbil.upenn.edu/epodb/ Genes expressed in vertebrate RBC
FlyView http://pbio07.uni-muenster.de/ Drosophila development and genetics
Gene Expression Database (GXD) http://www.informatics.jax.org/searches/gxdindex_form.shtml Mouse gene expression and genomics
Interferon Stimulated Gene Database http://www.lerner.ccf.org/labs/williams/xchip-html.cgi Genes induced by treatment with interferons
Kidney Development Database http://www.ana.ed.ac.uk/anatomy/database/kidbase/kidhome.html Kidney development and gene expression
MAGEST http://star.scl.kyoto-u.ac.jp/magest/ Ascidian (Halocynthia roretzi) gene expression patterns
MethDB http://www.methdb.de DNA methylation data, patterns and profiles
Mouse Atlas and Gene Expression Database http://genex.hgu.mrc.ac.uk Spatially-mapped gene expression data
PEDB http://chroma.mbt.washington.edu/PEDB/ Normal and aberrant prostate gene expression
RECODE http://recode.genetics.utah.edu Genes using programmed translational recoding in their expression
Stanford Microarray Database http://genome-www.stanford.edu/microarray Raw and normalized data from microarray experiments
TRIPLES http://ygac.med.yale.edu/triples/triples.htm TRansposon-Insertion Phenotypes, Localization, and Expression in Saccharomyces
Tooth Development Database http://bite-it.helsinki.fi/ Gene expression in dental tissue
Gene Identification and Structure
AllGenes http://www.allgenes.org Human and mouse gene index integrating gene, transcript and protein annotation
Ares Lab Intron Site http://www.cse.ucsc.edu/research/compbio/yeast_introns.html Yeast spliceosomal introns
AsMamDB http://166.111.30.65/ASMAMDB.html Alternatively-spliced mammalian genes
COMPEL http://compel.bionet.nsc.ru/ Composite regulatory elements
CUTG http://www.kazusa.or.jp/codon/ Codon usage tables
DBTBS http://elmo.ims.u-tokyo.ac.jp/dbtbs/ Bacillus subtilis binding factors and promoters
EID http://mcb.harvard.edu/gilbert/EID/ Protein-coding, intron-containing genes
EPD http://www.epd.isb-sib.ch/ Eukaryotic POL II promoters with experimentally-determined transcription start sites
ExInt http://intron.bic.nus.edu.sg/exint/exint.html Exon-intron structure of eukaryotic genes
HUNT http://www.hri.co.jp/HUNT Annotated human full-length cDNA sequences
IDB/IEDB http://nutmeg.bio.indiana.edu/intron/index.html Intron sequence and evolution
PLACE http://www.dna.affrc.go.jp/htdocs/PLACE Plant cis-acting regulatory elements
PlantCARE http://sphinx.rug.ac.be:8080/PlantCARE/index.htm Plant cis-acting regulatory elements
PromEC http://bioinfo.md.huji.ac.il/marg/promec Escherichia coli mRNA promoters with experimentally identified transcriptional start sites
RRNDB http://rrndb.cme.msu.edu Variation in prokaryotic ribosomal RNA operons
STRBase http://www.cstl.nist.gov/div831/strbase/ Short tandem DNA repeats
SpliceDB http://genomic.sanger.ac.uk/spldb/SpliceDB.html Canonical and non-canonical mammalian splice sites
TRRD http://wwwmgs.bionet.nsc.ru/mgs/dbases/trrd4 Transcription regulatory regions of eukaryotic genes
TransTerm http://uther.otago.ac.nz/Transterm.html Codon usage, start and stop signals
VIDA http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html Virus genome open reading frames
WormBase http://www.wormbase.org Guide to Caernorhabditis elegans biology
YIDB http://www.EMBL-Heidelberg.DE/ExternalInfo/seraphin/yidb.html Yeast nuclear and mitochondrial intron sequences
rSNP Guide http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/ Single nucleotide polymorphisms in regulatory gene regions
Genetic and Physical Maps
DRESH http://www.tigem.it/LOCAL/drosophila/dros.html Human cDNA clones homologous to Drosophila mutant genes
G3-RH http://www-shgc.stanford.edu/RH/ Stanford G3 and TNG radiation hybrid maps
GB4-RH http://www.sanger.ac.uk/Software/RHserver//Rhserver.shtml Genebridge4 (GB4) human radiation hybrid maps
GDB http://www.gdb.org Human genes and genomic maps
GenAtlas http://www.citi2.fr/GENATLAS/ Human genes, markers and phenotypes
GenMapDB http://genomics.med.upenn.edu/genmapdb Mapped human BAC clones
GeneMap ‘99 http://www.ncbi.nlm.nih.gov/genemap/ International Radiation Mapping Consortium human gene map
HuGeMap http://www.infobiogen.fr/services/Hugemap Human genome genetic and physical map data
IXDB http://ixdb.mpimg-berlin-dahlem.mpg.de Physical maps of human chromosome X
RHdb http://www.ebi.ac.uk/RHdb Radiation hybrid map data
Radiation Hybrid Database http://www.ebi.ac.uk/RHdb Radiation hybrid map data
Genomic Databases
ACeDB http://www.sanger.ac.uk/Software/Acedb/ C.elegans, Saccharomyces pombe, and human sequences and genomic information
AMmtDB http://bio-www.ba.cnr.it:8000/BioWWW/#AMMTDB Metazoan mitochondrial DNA sequences
ArkDB http://www.thearkdb.org/genome_mapping.html Genome databases for farm and other animals
Comprehensive Microbial Resource http://www.tigr.org/tigr-scripts/CMR2/CMRHomePage.spl Completed microbial genomes
CropNet http://ukcrop.net/ Genome mapping in crop plants
CyanoBase http://www.kazusa.or.jp/cyano/ Synechocystis sp. genome
EMGlib http://pbil.univ-lyon1.fr/emglib/emglib.html Completely sequenced microbial genomes from bacteria, archaea, yeast
EcoGene http://bmb.med.miami.edu/EcoGene/EcoWeb/ E.coli K-12 sequences
FlyBase http://www.fruitfly.org Drosophila sequences and genomic information
Full-Malaria http://133.11.149.55 Full-length cDNA library from erythrocytic-stage Plasmodium falciparum
GOBASE http://megasun.bch.umontreal.ca/gobase/gobase.html Organelle genome database
GOLD http://igweb.integratedgenomics.com/GOLD/ Information regarding complete and ongoing genome projects
HIV Sequence Database http://hiv-web.lanl.gov/ HIV RNA sequences
Human BAC Ends Database http://www.tigr.org/tdb/humgen/bac_end_search/bac_end_intro.html Non-redundant human BAC end sequences
ICB http://www.mbio.co.jp/icb Identification and classification of bacteria using protein-coding
INE http://rgp.dna.affrc.go.jp/giot/INE.html Rice genetic and physical maps and sequence data
MITOMAP http://www.gen.emory.edu/mitomap.html Human mitochondrial genome
MITOP http://websvr.mips.biochem.mpg.de/proj/medgen/mitop Mitochondrial proteins, genes, and diseases
Medicago Genome Initiative http://www.noble.org/medicago/ Model legume Medicago truncatula ESTs, gene expression and proteomic data
Mendel Database http://jiio6.jic.bbsrc.ac.uk/ Database of plant EST and STS sequences annotated with gene family information
MitBASE http://www3.ebi.ac.uk/Research/Mitbase/mitbase.pl Mitochondrial genomes, intra-species variants, and mutants
MitoDat http://www-lecb.ncifcrf.gov/mitoDat/ Mitochondrial proteins (predominantly human)
MitoNuc/MitoAln http://bio-www.ba.cnr.it:8000/srs6/ Nuclear genes coding for mitochondrial proteins
Mouse Genome Database (MGD) http://www.informatics.jax.org Mouse genetics and genomics
Munich Information Center for Protein Sequences (MIPS) http://www.mips.biochem.mpg.de/ Protein and genomic sequences
NRSub http://pbil.univ-lyon1.fr/nrsub/nrsub.html B.subtilis genome
PlasmoDB http://PlasmoDB.org Plasmodium GENOME
RsGDB http://www-mmg.med.uth.tmc.edu/sphaeroides Rhodobacter sphaeroides genome
Saccharomyces Genome Database (SGD) http://genome-www.stanford.edu/Saccharomyces S.cerevisiae genome
TIGR Microbial Database http://www.tigr.org/tdb/mdb/mdbcomplete.html Microbual genomes and chromosomes
The Arabidopsis Information Resource (TAIR) http://www.arabidopsis.org/ Arabidopsis thaliana genome
ZFIN http://www.zfin.org Genetic, genomic and developmental data from zebrafish
ZmDB http://zmdb.iastate.edu/ Maize genome database
Intermolecular Interactions
Biomolecular Interaction Network Database (BIND) http://binddb.org Molecular interactions, complexes and pathways
DIP http://dip.doe-mbi.ucla.edu/ Catalog of protein–protein interactions
DPInteract http://arep.med.harvard.edu/dpinteract/ Binding sites for E.coli DNA-binding proteins
Database of Ribosomal Crosslinks (DRC) http://www.mpimg-berlin-dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc/ Ribosomal crosslinking data
Metabolic Pathways and Cellular Regulation
ENZYME http://www.expasy.ch/enzyme/ Enzyme nomenclature
EcoCyc http://ecocyc.pangeasystems.com/ecocyc/ E.coli K-12 genome, gene products, and metabolic pathways
EpoDB http://www.cbil.upenn.edu/EpoDB/ Genes expressed during human erythropoiesis
FlyNets http://gifts.univ-mrs.fr/FlyNets/FlyNets_home_page.html Drosophila melanogaster molecular interactions
Klotho http://www.ibc.wustl.edu/klotho/ Collection and categorization of biological compounds
Kyoto Encyclopedia of Genes and Genomes (KEGG) http://www.genome.ad.jp/kegg Metabolic and regulatory pathways
LIGAND http://www.genome.ad.jp/dbget/ligand.html Enzymatic ligands, substrates and reactions
RegulonDB http://www.cifn.unam.mx/Computational_Biology/regulondb/ E.coli transcriptional regulation and operon organization
UM-BBD http://www.labmed.umn.edu/umbbd/ Microbial biocatalytic reactions and biodegradation pathways
WIT2 http://wit.mcs.anl.gov/WIT2/ Integrated system for functional curation and development of metabolic models
Mutation Databases
16S and 23S Ribosomal RNA Mutation Databases http://ribosome.fandm.edu 16S and 23S ribosomal RNA mutation database
ALFRED http://alfred.med.yale.edu/alfred/index.asp Allele frequencies and DNA polymorphisms
Androgen Receptor Gene Mutations Database http://www.mcgill.ca/androgendb/ Mutations in the androgen receptor gene
Asthma Gene Database http://cooke.gsf.de/asthmagen/main.cfm Linkage and mutation studies on the genetics of asthma and allergy
Asthma and Allergy Database http://cooke.gsf.de/asthmagen/main.cfm
Atlas of Genetics and Cytogenetics in Oncology and Haematology http://www.infobiogen.fr/services/chromcancer/ Chromosomal abnormalities in cancer
BTKbase http://www.uta.fi/laitokset/imt/bioinfo/BTKbase/ Mutation registry for X-linked agammaglobulinemia
CASRDB http://data.mch.mcgill.ca/casrdb/ CASR mutations causing FHH, NSHPT and ADH
Cytokine Gene Polymorphism Database http://www.pam.bris.ac.uk/services/GAI/cytokine4.htm Cytokine gene polymorphisms, in vitro expression and disease-association studies
Database of Germline p53 Mutations http://www.lf2.cuni.cz/win/projects/germline_mut_p53.htm Mutations in human tumor and cell line p53 gene
GRAP Mutant Databases http://tinyGRAP.uit.no/GRAP/ Mutants of family A G-Protein Coupled Receptors (GRAP)
HGBASE http://hgbase.cgr.ki.se Intragenic sequence polymorphisms
HIV-RT http://hivdb.stanford.edu/hiv/ HIV reverse transcriptase and protease sequence variation
Haemophila B Mutation Database http://www.umds.ac.uk/molgen/haemBdatabase.htm Point mutations, short additions and deletions in the Factor IX gene
Human Gene Mutation Database (HGMD) http://www.uwcm.ac.uk/uwcm/mg/hgmd0.html Known (published) gene lesions underlying human inherited disease
Human PAX2 Allelic Variant Database http://www.hgu.mrc.ac.uk/Softdata/PAX2/ Mutations in human PAX2 gene
Human PAX6 Allelic Variant Database http://www.hgu.mrc.ac.uk/Softdata/PAX6/ Mutations in human PAX6 gene
Human Type I and Type III Collagen Mutation Database http://www.le.ac.uk/genetics/collagen/ Human type I and type III collagen gene mutations
HvrBase http://db.eva.mpg.de/Hvrbase/ Primate mtDNA control region sequences
KMDB http://mutview.dmb.med.keio.ac.jp/mutview3/kmeyedb/index.html Mutations in human eye disease genes
KinMutBase http://www.uta.fi/imt/bioinfo/KinMutBase/ Disease-causing protein kinase mutations
MmtDB http://www.ba.cnr.it/~areamt08/MmtDBWWW.htm Mutations and polymorphisms in metazoan mitochondrial DNA sequences
Mutation Spectra Database http://info.med.yale.edu/mutbase/ Mutations in viral, bacterial, yeast and mammalian genes
NCL Mutations http://www.ucl.ac.uk/ncl/ Mutations and polymorphisms in neuronal ceroid lipofuscinoses (NCL) genes
Online Mendelian Inheritance in Man http://www.ncbi.nlm.nih.gov/Omim/ Catalog of human genetic and genomic disorders
PAHdb http://www.mcgill.ca/pahdb/ Mutations at the phenylalanine hydroxylase locus
PHEXdb http://data.mch.mcgill.ca/phexdb Mutations in PHEX gene causing X-linked hypophosphatemia
PMD http://pmd.ddbj.nig.ac.jp/ Compilation of protein mutant data
PTCH1 Mutation Database http://www.cybergene.se/PTCH/ptchbase.html Mutations and SNPs found in PTCH1
RB1 Gene Mutation Database http://www.d-lohmann.de/Rb/ Mutations in the human retinoblastoma (RB1) gene
Ribosomal RNA Mutational Database http://ribosome.fandm.edu/ 16S and 23S ribosomal RNA mutation database
SV40 Large T-Antigen Mutant Database http://bigdaddy.bio.pitt.edu/SV40/ Mutations in SV40 large tumor antigen gene
dbSNP http://www.ncbi.nlm.nih.gov/SNP/ Single nucleotide polymorphisms
iARC p53 Database http://www.iarc.fr/p53/ Missense mutations and small deletions in human p53 reported in peer-reviewed literature
p53 Databases http://metalab.unc.edu/dnam/mainpage.html Mutations at the human p53 and hprt genes; rodent transgenic lacI and lacZ mutations
Pathology
FIMM http://sdmc.krdl.org.sg:8080/fimm/ Functional molecular immunology data
HCForum http://hcforum.imag.fr/welcome_eng.html Human cytogenetics database
Mouse Tumor Biology Database (MTB) http://tumor.informatics.jax.org Mouse tumor names, classification, incidence, pathology, genetic factors
Oral Cancer Gene Database http://www.tumor-gene.org/Oral/oral.html Cellular, molecular and biological data for genes involved in oral cancer
PEDB http://chroma.mbt.washington.edu/PEDB/ Sequences from prostate tissue and cell type-specific cDNA libraries
Tumor Gene Family Databases (TGDBs) http://www.tumor-gene.org/tgdf.html Cellular, molecular, and biological data about genes involved in various cancers
Protein Databases
AARSDB http://rose.man.poznan.pl/aars/index.html Aminoacyl-tRNA synthetase sequences
ABCdb http://ir2lcb.cnrs-mrs.fr/ABCdb/ ABC transporters
DAtA http://luggagefast.Stanford.EDU/group/arabprotein/ Annotated coding sequences from Arabidopsis
DExH/D Family Database http://www.columbia.edu/~ej67/dbhome.htm DEAD-box, DEAH-box and DExH-box proteins
ESTHER http://www.ensam.inra.fr/cholinesterase/ Esterases and alpha/beta hydrolase enzymes and relatives
Endogenous GPCR List http://www.biomedcomp.com/GPCR.html G protein-coupled receptors; expression in cell lines
FUNPEP http://www.gpcr.org/FUNPEP/db Low-complexity or compositionally-biased protein sequences
GPCRDB http://swift.embl-heidelberg.de/7tm/ G protein-coupled receptors
GenProtEC http://genprotec.mbl.edu Escherichia coli K-12 genome, gene products and homologs
HIV Molecular Immunology Database http://hiv-web.lanl.gov/immunology/ HIV epitopes
HUGE http://www.kazusa.or.jp/huge/ Large (50 kDa) human proteins and cDNA sequences
Histone Database http://genome.nhgri.nih.gov/histones/ Histone and histone fold sequences and structures
Homeobox Page http://copan.bioz.unibas.ch/homeo.html Information relevant to homeobox proteins, classification and evolution
Homeodomain Resource http://genome.nhgri.nih.gov/homeodomain Homeodomain sequences, structures, and related genetic and genomic information
IMGT http://imgt.cines.fr:8104/ Immunoglobulin, T cell receptor and MHC sequences from human and other vertebrates
IMGT/HLA http://www.ebi.ac.uk/imgt/hla/ Human major histocompatibility complexes
InBase http://www.neb.com/neb/inteins.html Intervening protein sequences (inteins) and motifs
Kabat Database http://immuno.bme.nwu.edu/ Sequences of proteins of immunological interest
LGICdb http://www.pasteur.fr/recherche/banques/LGIC/LGIC.html Ligand-gated ion channel subunit sequences
MEROPS http://www.merops.co.uk Proteolytic enzymes (proteases/peptidases)
MHCPEP http://wehih.wehi.edu.au/mhcpep/ MHC-binding peptides
Membrane Protein Database http://biophys.bio.tuat.ac.jp/ohshima/database/ Membrane protein sequences, transmembrane regions and structures
MetaFam http://metafam.ahc.umn.edu/ Integrated protein family information
Nuclear Receptor Resource http://nrr.georgetown.edu/nrr/nrr.html Nuclear receptor superfamily
Olfactory Receptor Database http://ycmi.med.yale.edu/senselab/ordb/ Sequences for olfactory receptor-like molecules
PKR http://pkr.sdsc.edu Protein kinase sequences, enzymology, genetics, and molecular and structural properties
PPMdb http://sphinx.rug.ac.be:8080/ppmdb/index.html Arabidopsis plasma membrane protein sequence and expression data
PROMISE http://bioinf.leeds.ac.uk/promise/ Prosthetic centers and metal ions in protein active sites
Peptaibol http://www.cryst.bbk.ac.uk/peptaibol/welcome.html Peptaibol (antibiotic peptide) sequences
PhosphoBase http://www.cbs.dtu.dk/databases/PhosphoBase/ Protein phosphorylation sites
PlantsP http://PlantsP.sdsc.edu Plant protein kinases and protein phosphatases
Prolysis http://delphi.phys.univ-tours.fr/Prolysis/ Proteases and natural and synthetic protease inhibitors
Protein Information Resource (PIR) http://pir.georgetown.edu Comprehensive, annotated, non-redundant protein sequence database
Ribonuclease P Database http://www.mbio.ncsu.edu/RNaseP/home.html RNase P sequences, alignments and structures
SENTRA http://wit.mcs.anl.gov/WIT2/Sentra/HTML/sentra.html Sensory signal transduction proteins
SWISS-PROT/TrEMBL http://www.expasy.ch/sprot Curated protein sequences
TIGRFAMs http://www.tigr.org/TIGRFAMs Protein family resource for the functional identification of proteins
TRANSFAC http://transfac.gbf.de/TRANSFAC/index.html Transcription factors and binding sites
Wnt Database http://www.stanford.edu/~rnusse/wntwindow.html Wnt proteins and phenotypes
ooTFD http://www.ifti.org/ Transcription factors and gene expression
trEST, trGEN and Hits http://hits.isb-sib.ch Predicted protein sequences
Protein Sequence Motifs
BLOCKS http://blocks.fhcrc.org/ Conserved sequence regions of protein families
CluSTr http://www.ebi.ac.uk/clustr/ Automatic classification of SWISS-PROT+TrEMBL proteins into related groups
InterPro http://www.ebi.ac.uk/interpro/ Integrated documentation resource for protein families, domains and sites
O-GLYCBASE http://www.cbs.dtu.dk/databases/OGLYCBASE/ Glycoproteins and O-linked glycosylation sites
PIR-ALN http://www-nbrf.georgetown.edu/pirwww/dbinfo/piraln.html Protein sequence alignments
PRINTS http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/ Hierarchical gene family fingerprints
PROSITE http://www.expasy.ch/prosite/ Biologically-significant protein patterns and profiles
Pfam http://www.sanger.ac.uk/Software/Pfam/ Multiple sequence alignments and hidden Markov models of common protein domains
ProClass http://pir.georgeown.edu/gfserver/proclass.html Protein families defined by PIR superfamilies and PROSITE patterns
ProDom http://www.toulouse.inra.fr/prodom.html Protein domain families
ProtoMap http://www.protomap.cs.huji.ac.il/ Automated hierarchical classification of SWISS- PROT proteins
SBASE http://www3.icgeb.trieste.it/~sbasesrv/ Annotated protein domain sequences
SMART http://smart.embl-heidelberg.de/ Signaling domain sequences
SYSTERS http://www.dkfz-heidelberg.de/tbi/services/cluster/systersform Classification of protein sequences into disjoint clusters with annotations from various other resources
eMOTIF http://motif.stanford.edu/emotif Protein sequence motif determination and searches
iPROCLASS http://pir.georgetown.edu/iproclass/ Annotated protein classification database
Proteome Resources
AAindex http://www.genome.ad.jp/dbget/ Physicochemical properties of peptides
Proteome Analysis Database http://www.ebi.ac.uk/proteome/ Online application of interpro and clustr for the functional classification of proteins in whole genomes
REBASE http://rebase.neb.com/rebase/rebase.html Restriction enzymes and associated methylases
SWISS-2DPAGE http://www.expasy.ch/ch2d/ Annotated two-dimensional polyacrylamide gel electrophoresis database
Yeast Proteome Database (YPD) http://www.proteome.com/databases/index.html S.cerevisiae proteome
RNA Sequences
5S Ribosomal RNA Database http://biobases.ibch.poznan.pl/5SData/ 5S rRNA sequences
ACTIVITY http://wwwmgs.bionet.nsc.ru/mgs/systems/activity/ Functional DNA/RNA site activity
ARED http://rc.kfshrc.edu.sa AU-rich element-containing mRNAs
Collection of mRNA-like Noncoding RNAs http://biobases.ibch.poznan.pl/ncRNA/ Non-protein-coding RNA transcripts
European Large Subunit Ribosomal RNA Database http://rrna.uia.ac.be/lsu/index.html Alignment of large subunit ribosomal RNA sequences with secondary structure information
European Small Subunit Ribosomal RNA Database http://rrna.uia.ac.be/ssu/index.html Alignment of small subunit ribosomal RNA sequences with secondary structure information
Guide RNA Database http://www.biochem.mpg.de/~goeringe/ Guide RNA sequences
HyPaLib http://bibiserv.techfak.uni-bielefeld.de/HyPa/ Structural elements characteristic for classes of RNA
Intronerator http://www.cse.ucsc.edu/~kent/intronerator/ RNA splicing and gene structure in C.elegans; alignments of Caernorhabditis briggsae and C.elegans genomic sequences
Non-Canonical Interactions in RNA http://prion.bchs.uh.edu/bp_type/ Non-standard base-base interactions in known RNA structures
PLMItRNA http://bigarea.area.ba.cnr.it:8000/PLMItRNA/ Mitochondrial tRNA genes and molecules in photosynthetic eukaryotes
Pseudobase http://wwwbio.leidenuniv.nl/~Batenburg/PKB.html Information on RNA pseudoknots
RISCC http://ulises.umh.es/RISSC Ribosomal 16S-23S RNA gene spacer regions
RNA Modification Database http://medlib.med.utah.edu/RNAmods/ Naturally modified nucleosides in RNA
Ribosomal Database Project (RDP) http://rdp.cme.msu.edu/ rRNA sequences, alignments and phylogenies
SELEXdb http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/ Selected DNA/RNA functional site sequences
SRPDB http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html Signal recognition particle RNA, protein and receptor sequences
Small RNA Database http://mbcr.bcm.tmc.edu/smallRNA Direct sequencing of small RNA sequences from prokaryotes and eukaryotes
The tmRNA Website http://www.indiana.edu/~tmrna tmRNA sequences, foldings and alignments
UTRdb/UTRsite http://bigarea.area.ba.cnr.it:8000/EmbIT/UTRHome/ 5'’ and 3'’ UTRs of eukaryotic mRNAs and relevant functional patterns
Viroids and viroid-like RNAs http://nt.ars-grin.gov/subviral/ Viroids and viroid-like RNAs
Yeast snoRNA Database http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html Yeast small nucleolar RNA
tRNA Sequences http://www.uni-bayreuth.de/departments/biochemie/trna/ TRNA and tRNA gene sequences
tmRDB http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html TmRNA (10Sa RNA) sequences
Retrieval Systems and Database Structure
KEYnet http://www.ba.cnr.it/keynet.html Hierarchical list of gene and protein names for data retrieval
TESS http://www.cbil.upenn.edu/tess Transcription element search system
Virgil http://www.infobiogen.fr/services/virgil Database interconnectivity
Structure
ASTRAL http://astral.stanford.edu/ Sequences of domains of known structure, selected subsets and sequence-structure correspondences
BioImage http://www-embl.bioimage.org/ Searchable database of multidimensional biological images
BioMagResBank http://www.bmrb.wisc.edu/ NMR spectroscopic data from proteins, peptides and nucleic acids
CATH http://www.biochem.ucl.ac.uk/bsm/cath/ Hierarchical classification of protein domain structures
CE http://cl.sdsc.edu/ce.html CE: A Resource to Compute and Review 3-D Protein Structure Alignments
CKAAPs DB http://cl.sdsc.edu/ckaap Structurally-similar proteins with dissimilar sequences
CSD http://www.ccdc.cam.ac.uk/prods/csd/csd.html Crystal structure information for organic and metal organic compounds
Database of Macromolecular Movements http://bioinfo.mbb.yale.edu/MolMovDB/ Descriptions of protein and macromolecular motions, including movies
Decoys ‘R’ Us http://dd.stanford.edu/ Computer-generated protein conformations based on sequence data
HIC-Up http://alpha2.bmc.uu.se/hicup/ Structures of small molecules (hetero-compounds)
HSSP http://www.sander.ebi.ac.uk/hssp/ Structural families and alignments; structurally-conserved regions and domain architecture
IMB Jena Image Library of Biological Macromolecules http://www.imb-jena.de/IMAGE.html Visualization and analysis of three-dimensional biopolymer structures
ISSD http://www.protein.bio.msu.su/issd/ Integrated sequence and structural information
LPFC http://www-smi.stanford.edu/projects/helix/LPFC/ Library of protein family core structures
MMDB http://www.ncbi.nlm.nih.gov/Structure/ All experimentally-determined three-dimensional structures, linked to NCBI Entrez
ModBase http://pipe.rockefeller.edu/modbase Annotated comparative protein structure models
NDB http://ndbserver.rutgers.edu/NDB/ndb.html Nucleic acid-containing structures
NTDB http://ntdb.chem.cuhk.edu.hk Thermodynamic data for nucleic acids
PALI http://pauling.mbu.iisc.ernet.in/~pali Phylogeny and alignment of homologous protein structures
PDB http://www.rcsb.org/pdb/ Structure data determined by X-ray crystallography and NMR
PDB-REPRDB http://www.rwcp.or.jp/papia/ Representative protein chains, based on PDB entries
PDBsum http://www.biochem.ucl.ac.uk/bsm/pdbsum Summaries and analyses of PDB structures
PRESAGE http://presage.berkeley.edu/ Protein structures with experimental and predictive annotations
ProTherm http://www.rtc.riken.go.jp/jouhou/protherm/protherm.html Thermodynamic data for wild-type and mutant proteins
RESID http://www-nbrf.georgetown.edu/pirwww/dbinfo/resid.html Protein structure modifications
SCOP http://scop.mrc-lmb.cam.ac.uk/scop/ Familial and structural protein relationships
SLoop http://www-cryst.bioc.cam.ac.uk/~sloop/ Classification of protein loops
Transgenics
Cre Transgenic Database http://www.mshri.on.ca/nagy/cre.htm Cre transgenic mouse lines
Transgenic/Targeted Mutation Database http://tbase.jax.org/ Information on transgenic animals and targeted mutations
Varied Biomedical Content
BAliBASE http://www-igbmc.u-strasbg.fr/BioInfo/BaliBASE2/index.html Benchmark database for comparison of multiple sequence alignments
DBcat http://www.infobiogen.fr/services/dbcat/ Catalog of databases
DrugDB http://pharminfo.com/drugdb/db_mnu.html Pharmacologically-active compounds; generic and trade names
END http://www.ibc.wustl.edu/biognosis/agora_interface/html/agora_entrance.html Enzyme nomenclature
Global Image Database http://www.gwer.ch/qv/gid/gid.htm Annotated biological images
GlycoSuiteDB http://www.glycosuite.com N- and O-linked glycan structures and biological source information
HOX-PRO http://www.mssm.edu/molbio/hoxpro/new/hox-pro00.html Clustering of homeobox genes
Imprinted Genes and Parent-of-Origin Effects http://www.otago.ac.nz/IGC Imprinted genes and parent-of-origin effects in animals
LocusLink/RefSeq http://www.ncbi.nlm.nih.gov/LocusLink/ Curated sequence and descriptive information about genetic loci
MPDB http://www.biotech.ist.unige.it/interlab/mpdb.html Information on synthetic oligonucleotides proven useful as primers or probes
Molecular Probe Database http://srs.ebi.ac.uk/ Synthetic oligonucleotides, probes and PCR primers
NCBI Taxonomy Browser http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html Names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence
PubMed http://www.ncbi.nlm.nih.gov/PubMed/ MEDLINE and Pre-MEDLINE citations
Tree of Life http://phylogeny.arizona.edu/tree/phylogeny.html Information on phylogeny and biodiversity
Vectordb
 http://vectordb.atcg.com/
 Characterization and classification of nucleic acid vectors





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