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2009 NAR Database Summary Papers

Nucleotide Sequence Databases

International Nucleotide Sequence Database Collaboration

DDBJ - DNA Data Bank of Japan

EMBL Nucleotide Sequence Database

Coding and non-coding DNA

ACLAME - A Classification of Mobile genetic Elements

Ciliate IES-MDS database

CORG - A database for COmparative Regulatory Genomics

CUTG - Codon Usage Tabulated from GenBank

MICdb - Database of Prokaryotic Microsatellites

NPRD - Nucleosome Positioning Region Database

OriDB - The DNA Replication Origin Database

Synthetic Gene Database

TIGR plant repeat database

TIGR Plant Transcript Assembly database

UCbase and miRfunc

VISTA Enhancer Browser

Gene structure, introns and exons, splice sites

ASDB - Alternative Splicing Database

EDAS - EST-Derived Alternative Splicing Database

EID: Exon-Intron Database

FESD - Functional Element SNPs Database

HS³D - Homo Sapiens Splice Sites Dataset

Yeast Intron Database

Transcriptional regulator sites and transcription factors

AGRIS - Arabidopsis Gene Regulatory Information Server

Cancer Chromosomes

CTCF Binding Site Database

DoOP - Databases of Orthologous Promoters

ODB - Operon database

Osteo-Promoter Database

Plant Stress-Responsive Gene Catalog

PPDB: Plant Promoter Database

PTM-Switchboard

SCPD - Saccharomyces cerevisiae promoter database

SKY/M-FISH and CGH

Telomerase database

TRED - Transcriptional Regulatory Element Database

VISTA Enhancer Browser

RNA sequence databases

16S and 23S Ribosomal RNA Mutation Database

3D rRNA modification maps

5S Ribosomal RNA Database

Aptamer Database

Cereal Small RNA Database

CORG - A database for COmparative Regulatory Genomics

European rRNA database

GtRDB - Genomic tRNA Database

HIV Sequence Database

HuSiDa - Human siRNA database

IRESdb - the Internal Ribosome Entry Site database

Mobile group II introns database

NCIR - Non-Canonical Interactions in RNA

ncRNAs database

Plant snoRNA DB

Ribosomal Database Project (RDP-II)

RISSC - Ribosomal Internal Spacer Sequence Collection

RNA Modification Database

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data

Subviral RNA Database

The Small Subunit rRNA Modification Database

The tmRNA website

Yeast snoRNA Database

Protein sequence databases

General sequence databases

NCBI Protein database

PIR - Protein Information Resource

Swiss-Prot (UniProtKB\Swiss-Prot)

Protein properties

PFD - Protein Folding Database

Protein localization and targeting

DBSubLoc - Database of protein Subcellular Localization

eSLDB - eukaryotic Subcellular Localization database

NMPdb - Nuclear matrix associated proteins database

NOPdb: Nucleolar Proteome Database

NPD - Nuclear Protein Database

Nuclear Receptor Resource

OGRe - Organellar Genome Retrieval

Secreted Protein Database

THGS - Transmembrane Helices in Genome Sequences

TransMembrane Protein DataBase

Protein sequence motifs and active sites

ASC - Active Sequence Collection

COMe - Co-Ordination of Metals etc.

CSA - Catalytic Site Atlas

eF-site - Electrostatic surface of Functional site

Metalloprotein Site Database

Minimotif Miner

Protein domain databases; protein classification

ADDA - A Domain Database

COG - Clusters of Orthologous Groups of proteins

DomIns - Database of Domain Insertions

EVEREST - EVolutionary Ensembles of REcurrent SegmenTs

Protein Clusters

Protein Segment Finder

Databases of individual protein families

Aminoacyl-tRNA synthetase database

Animal Toxin Database

CSDBase - Cold Shock Domain database

DCCP - Database of Copper-Chelating Proteins

Defensins Knowledgebase

Degradome Database

DExH/D Family Database

Endogenous GPCR List

GPCR NaVa database

gpDB - G-protein database

Heme Protein Database

Histone Database

HIV RT and Protease Sequence Database

Homeodomain Resource

Knottin database

Lipase Engineering Database

Nuclear Receptor Resource

Olfactory Receptor Database

PlantsP/PlantsT

ProLysED - Prokaryotic Lysis Enzymes Database

Protein kinase resource

Ribonuclease P Database

RPG - Ribosomal Protein Gene database

RTKdb - Receptor Tyrosine Kinase database

Telomerase database

UCSD-Nature Signaling Gateway Molecule Pages

VKCDB - Voltage-gated K⁺ Channel Database

Structure Databases

Small molecules

AANT - Amino Acid - Nucleotide interaction database

ChEBI - Chemical Entities of Biological Interest

CSD - Cambridge Structural Database

BCSDB/Glycoscience

CCSD - Complex Carbohydrate Structure Database (CarbBank)

CSS - Carbohydrate Structure Suite

Glycoconjugate Data Bank

Monosaccharide Browser

Nucleic acid structure

NCIR - Non-Canonical Interactions in RNA

SARS-CoV RNA SSS

SCOR - Structural Classification Of RNA

Protein structure

3DID - 3D interacting domains

CADB - Conformational Angles DataBase of Proteins

CSA - Catalytic Site Atlas

DisProt - Database of Protein Disorder

DomIns - Database of Domain Insertions

DSDBASE - Disulfide Database

DSMM - a Database of Simulated Molecular Motions

E-MSD - EBI-Macromolecular Structure Database

eF-site - Electrostatic surface of Functional site

Genomic Threading Database

GTOP - Genomes To Protein structures

HOMSTRAD - Homologous Structure Alignment Database

IMGT/3Dstructure-DB

Jenalib: Jena Library of Biological Macromolecules

MolMovDB - Database of Macromolecular Movements

PFD - Protein Folding Database

PMDB - Protein Model Database

S4: Structure-based Sequence Alignments of SCOP Superfamilies

SCOP - Structural Classification Of Proteins

SSToSS - Sequence-Structural Templates of Single-member Superfamilies

Structure Superposition Database

SWISS-MODEL Repository

TOPS - Topology Of Protein Structures

Genomics Databases (non-vertebrate)

MGD - Mouse Genome Database

TIGR Gene Indices

Genome annotation terms, ontologies and nomenclature

GO - Gene Ontology

GOA - Gene Ontology Annotation

IUBMB Nomenclature database

IUPAC Nomenclature database

Plant Ontology database

Taxonomy and identification

MICdb - Database of Prokaryotic Microsatellites

NCBI Taxonomy Browser

Ribosomal Database Project (RDP-II)

RIDOM - Ribosomal Differentiation of Medical Microorganisms

RISSC - Ribosomal Internal Spacer Sequence Collection

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data

General genomics databases

Animal Genome Size Database

Biodefense Proteomics Resource Center

COG - Clusters of Orthologous Groups of proteins

DEG - Database of Essential Genes

Genome information broker

Genome Project Database

GtRDB - Genomic tRNA Database

Integr8 (formerly Proteome Analysis Database)

KEGG - Kyoto Encyclopedia of Genes and Genomes

MBGD - Microbial Genome Database

NegProt - Negative Proteome database

NMPDR - National Microbial Pathogen Data Resource

PEP: Predictions for Entire Proteomes

TIGR Comprehensive Microbial Resource

TIGR Gene Indices

Viral genome databases

HCVDB - Hepatitis C Virus Database

HERVd - Human Endogenous Retrovirus database

HIV Drug Resistance Database

HIV Interactions database

HIV Molecular Immunology Database

HIV RT and Protease Sequence Database

HIV Sequence Database

Influenza Virus Resource

IVDB - Influenza Virus Database

NCBI Viral genomes

RNA Virus Database

SARS-CoV RNA SSS

Subviral RNA Database

T4-like genome database

The HIV Positive Selection Mutation Database

Viral Bioinformatics Resource

Prokaryotic genome databases

ASAP - A Systematic Annotation Package

BSORF - Bacillus subtilis Open Reading Frames

CCDB - The CyberCell Database

CIDB - Chlamydia Interactive Database

Comparative Genometrics

EMGlib - Enhanced Microbial Genomes Library

Essential genes in E. coli

HGT-DB, Horizontal Gene Transfer-DataBase

Interrupted coding sequences

ODB - Operon database

PAIDB - Pathogenicity Island Database

PEC - Profiling of E. coli Chromosome

PGTdb - Prokaryotic Growth Temperature database

Pseudomonas Genome Database

UCSC Archaeal Genome Browser

VFDB - Virulence Factors Database

VNTR Locus Database

Unicellular eukaryotes genome databases

ApiDB - Apicomplexan DataBase

Aspergillus Genomes

CryptoDB - Cryptosporidium database

Diatom EST Database

TGD - Tetrahymena Genome Database

ToxoDB - The Toxoplasma gondii Genome Database

Fungal genome databases

Magnaporthe grisea Database

AGD - Ashbya Genome Database

CADRE - Central Aspergillus Data Repository

Candida Genome Database

COGEME Phytopathogenic Fungi and Oomycete EST Database

CYGD - Comprehensive Yeast Genome Database

Fungal Genome Size Database

OGD - Oomycete Genomics Database

OriDB - The DNA Replication Origin Database

SCMD - Saccharomyces cerevisiae Morphological Database

SCPD - Saccharomyces cerevisiae promoter database

SGD - Saccharomyces Genome Database

VBI Microbial Database

YDPM - Yeast Deletion Project

Yeast Intron Database

Yeast Resource Center

Yeast snoRNA Database

yMGV - Yeast microarray global viewer

Invertebrate genome databases

Drosophila microarray centre

C. elegans Project

Drosophila polymorphism database

InterActive Fly

KinG - Kinases in Genomes

Pristionchus.org

WorfDB - Worm ORF Database

Metabolic and Signaling Pathways

Enzymes and enzyme nomenclature

Enzyme Nomenclature

Metabolic pathways

BRITE - Biomolecular Relations in Information Transmission and Expression

BSD - Biodegradative Strain Database

HMDB - The Human Metabolome Database

KEGG - Kyoto Encyclopedia of Genes and Genomes

NMPDR - National Microbial Pathogen Data Resource

Protein-protein interactions

ConsensusPathDB

DIP - Database of Interacting Proteins

DRC - Database of Ribosomal Crosslinks

DroID - Drosophila Interactions Database

Hedgehog signalling

HPID - Human Protein Interaction database

I2D - Interologous Interaction Database

Inter-Chain Beta-Sheets

MHC-Peptide Interaction Database

MiMI - Michigan Molecular Interactions

MiST - Microbial Signal Transduction database

PIG - Pathogen Interaction Gateway

Protein kinase resource

Protein-protein interfaces

STCDB - Signal Transduction Classification Database

The Cell Cycle DB

Signalling pathways

UCSD-Nature Signaling Gateway Molecule Pages

Human and other Vertebrate Genomes

Model organisms, comparative genomics

ABA - Ascidian Body Atlas

Animal Genome Size Database

CORG - A database for COmparative Regulatory Genomics

Cre Transgenic Database

Edinburgh Mouse Atlas

EGO - Eukaryotic Gene Orthologs

GXD - Mouse Gene Expression Database

KOG - Eukaryotic Orthologous Groups of proteins

MGD - Mouse Genome Database

Mouse Phenome Database

Mouse Transposon Insertion Database

Mouse Tumor Biology Database

MUGEN Mouse Database

Non-Human Genome Segmental Duplication Database

OMIA - Online Mendelian Inheritance in Animals

PEDE - Pig Expression Data Explorer

Rat Genome Database

RTCGD - Retroviral Tagged Cancer Gene Database

TAED - The Adaptive Evolution Database

Human genome databases, maps and viewers

Cancer Chromosomes

ENCODE Project at UCSC

Human BAC Ends Database

Human Genome Segmental Duplication Database

The Chromosome 7 Annotation Project

UCSC Genome Browser

ASDB - Alternative Splicing Database

ENCODE Project at UCSC

HPRD - Human Protein Reference Database

HS³D - Homo Sapiens Splice Sites Dataset

HUGE - Human Unidentified Gene-Encoded large proteins

Human Proteinpedia

IPI - International Protein Index

Mammalian Gene Collection

TIGR Gene Indices

trome, trEST and trGEN

Human Genes and Diseases

Protein Mutant Database

General human genetics databases

Comparative Toxicogenomics Database

Genetics Home Reference

HAGR - Human Ageing Genomic Resources

HCAD - Human Chromosome Aberration Database

HERVd - Human Endogenous Retrovirus database

Human PAML Browser

MSY Breakpoint Mapper

OMIM - Online Mendelian Inheritance in Man

General polymorphism databases

Cypriot national mutation database

Database of Genomic Variants

IPD - Immuno Polymorphism Database

OMIM - Online Mendelian Inheritance in Man

TPMD - Taiwan polymorphic microsatellite marker database

Cancer gene databases

Atlas of Genetics and Cytogenetics in Oncology and Haematology

Cancer Chromosomes

CGED - Cancer Gene Expression Database

COSMIC - Catalogue Of Somatic Mutations In Cancer

Database of Germline p53 Mutations

Human p53, human hprt, rodent lacI and rodent lacZ databases

IARC TP53 Database

Mouse Tumor Biology Database

RTCGD - Retroviral Tagged Cancer Gene Database

SV40 Large T-Antigen Mutant Database

Tumor Associated Gene database

Tumor Gene Family Databases (TGDBs)

Gene-, system- or disease-specific databases

Androgen Receptor Gene Mutations Database

Atlas of Genetics and Cytogenetics in Oncology and Haematology

BGED - Brain Gene Expression Database

Collagen Mutation Database

Cytokine Gene Polymorphisms

DNAreplication.net

EICO DB - Expression-based Imprint Candidate Organiser

EpoDB - Erythropoiesis Database

ERGDB - Estrogen Responsive Genes Database

GOLD.db - Genomics Of Lipid-associated Disorders

HemoPDB - Hematopoietic Promoter Database

HORDE - Human Olfactory Receptor Data Exploratorium

HPMR - Human Plasma Membrane Receptome

Human PAX2 Allelic Variant Database

Human PAX6 Allelic Variant Database

Imprinted Gene Catalogue

Lowe Syndrome Mutation Database

Prostate Expression Database

PTCH1 Mutation Database

RB1 Gene Mutation Database

T1DBase - Type 1 Diabetes Database

The Autism Chromosome Rearrangement Database

The Lafora Database

Microarray Data and other Gene Expression Databases

Drosophila microarray centre

ABA - Ascidian Body Atlas

BGED - Brain Gene Expression Database

CATMA - Complete Arabidopsis Transcriptome MicroArray

CGED - Cancer Gene Expression Database

Edinburgh Mouse Atlas

EpoDB - Erythropoiesis Database

Gene Aging Nexus

Gene Expression in Tooth Database

GEO - Gene Expression Omnibus

GXD - Mouse Gene Expression Database

HemoPDB - Hematopoietic Promoter Database

HPMR - Human Plasma Membrane Receptome

HugeIndex - Human Gene Expression Index

Interferon Stimulated Gene Database

International Gene Trap Consortium Database

Kidney Development Database

MAMEP - Molecular Anatomy of the Mouse Embryo Project

MEPD: A Medaka gene expression pattern database

PEPR - Public Expression Profiling Resource

Prostate Expression Database

Stanford Microarray Database

yMGV - Yeast microarray global viewer

Proteomics Resources

Biodefense Proteomics Resource Center

Open Proteomics Database

PEP: Predictions for Entire Proteomes

Other Molecular Biology Databases

StrainInfo.net Bioportal

The Cell Cycle DB

University of Pittsburgh Bioinformatics Resources Collection

Drugs and drug design

APD - Antimicrobial Peptide Database

BSD - Biodegradative Strain Database

DART - Drug Adverse Reaction Targets

Defensins Knowledgebase

HIV Drug Resistance Database

HIV Molecular Immunology Database

SuperTarget and Matador

TTD - Therapeutic Target Database

Molecular probes and primers

MPDB - Molecular Probe Database

QPPD - Quantitative PCR Primer Database

Organelle databases

Chloroplast Genome Database

Organelle genomes

Plant Organelles Database

Mitochondrial genes and proteins

HmtDB - Human Mitochondrial DataBase

MPIM - Mitochondrial Protein Import Machinery

OGRe - Organellar Genome Retrieval

YDPM - Yeast Deletion Project

Plant databases

Chloroplast Genome Database

General plant databases

Cereal Small RNA Database

CR-EST - Crop ESTs

GénoPlante-Info

MPIM - Mitochondrial Protein Import Machinery

Plant DNA C-values database

Plant Genome Central

Plant Ontology database

Plant snoRNA DB

Plant Stress-Responsive Gene Catalog

PlantsP/PlantsT

PPDB: Plant Promoter Database

PPDB: Plant Proteomics Database

TAED - The Adaptive Evolution Database

TIGR plant repeat database

TIGR Plant Transcript Assembly database

Arabidopsis thaliana

AGNS - Arabidopsis GeneNet supplementary

AGRIS - Arabidopsis Gene Regulatory Information Server

Arabidopsis Hormone Database

Arabidopsis Mitochondrial Protein Database

Arabidopsis MPSS

Arabidopsis Nucleolar Protein Database

ASRP - Arabidopsis Small RNA Project

CATMA - Complete Arabidopsis Transcriptome MicroArray

RARGE - RIKEN Arabidopsis Genome Encyclopedia

The Arabidopsis Information Resource (TAIR)

Oryza Tag Line

BGI-RISe - Beijing Genomics Institute Rice Information System

IRIS - International Rice Information System

Rice Annotation Database

Rice Gene Thresher

Rice Mutant Database

Rice Proteome Database

Diatom EST Database

Genome Database for Rosaceae

Legume Information System

MtDB - Medicago trunculata Database

PoMaMo - Potato Maps and More

Shanghai Rapeseed Database

TED - Tomato Expression Database

TIGR Maize database

Immunological databases

Immune epitope database

Interferon Stimulated Gene Database

IPD-HPA - Human Platelet Antigens

IPD-KIR - Killer-cell Immunoglobulin-like Receptors

MHC-Peptide Interaction Database

MUGEN Mouse Database

Compilation Paper

Alphabetical List

Category/Paper List

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