《核酸研究》.2005年.第Da期

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• GenBank
• Entrez Gene: gene-centered information at NCBI
• The European Bioinformatics Institute's data resources: towards system
• Database resources of the National Center for Biotechnology Informatio
• TRED: a Transcriptional Regulatory Element Database and a platform for
• TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial
• siRNAdb: a database of siRNA sequences
• RNAdb—a comprehensive mammalian noncoding RNA database
• Rfam: annotating non-coding RNAs in complete genomes
• NONCODE: an integrated knowledge database of non-coding RNAs
• UTRdb and UTRsite: a collection of sequences and regulatory motifs of
• Compilation of tRNA sequences and sequences of tRNA genes
• The Small Subunit rRNA Modification Database
• NMPdb: Database of Nuclear Matrix Proteins
• CDD: a Conserved Domain Database for protein classification
• ADDA: a domain database with global coverage of the protein universe
• PDBSite: a database of the 3D structure of protein functional sites
• PRECISE: a Database of Predicted and Consensus Interaction Sites in En
• InterPro, progress and status in 2005
• FunShift: a database of function shift analysis on protein subfamilies
• S4: structure-based sequence alignments of SCOP superfamilies
• ProtoNet 4.0: A hierarchical classification of one million protein seq
• The ProDom database of protein domain families: more emphasis on 3D
• The RCSB Protein Data Bank: a redesigned query system and relational d
• REBASE—restriction enzymes and DNA methyltransferases
• The SYSTERS Protein Family Database in 2005
• The SBASE domain sequence resource, release 12: prediction of protein
• The CATH Domain Structure Database and related resources Gene3D and DH
• Carbohydrate Structure Suite(CSS): analysis of carbohydrate 3D struct
• PDB-Ligand: a ligand database based on PDB for the automated and custo
• E-MSD: an integrated data resource for bioinformatics
• IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobu
• Editorial
• Editorial
• DDBJ in collaboration with mass-sequencing teams on annotation
• The Molecular Biology Database Collection: 2005 update
• The EMBL Nucleotide Sequence Database
• GenDiS: Genomic Distribution of protein structural domain Superfamilie
• PFD: a database for the investigation of protein folding kinetics and
• PDB_TM: selection and membrane localization of transmembrane proteins
• STING Report: convenient web-based application for graphic and tabular
• PDBsum more: new summaries and analyses of the known 3D structures of
• ECgene: genome annotation for alternative splicing
• The TIGR Gene Indices: clustering and assembling EST and known genes a
• NPRD: Nucleosome Positioning Region Database
• HOPPSIGEN: a database of human and mouse processed pseudogenes
• The MAPPER database: a multi-genome catalog of putative transcription
• DoOP: Databases of Orthologous Promoters, collections of clusters of o
• SpliceInfo: an information repository for mRNA alternative splicing in
• HuSiDa—the human siRNA database: an open-access database for published
• The Universal Protein Resource(UniProt)
• PA-GOSUB: a searchable database of model organism protein sequences wi
• eBLOCKs: enumerating conserved protein blocks to achieve maximal sensi
• TPMD: a database and resources of microsatellite marker genotyped in T
• SPD—a web-based secreted protein database
• PSORTdb: a protein subcellular localization database for bacteria
• The PEDANT genome database in 2005
• PartiGeneDB—collating partial genomes
• The Ribosomal Database Project(RDP-II): sequences and tools for high-
• VFDB: a reference database for bacterial virulence factors
• The Ashbya Genome Database(AGD)—a tool for the yeast community and ge
• The Diatom EST Database
• Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating com
• CandidaDB: a genome database for Candida albicans pathogenomics
• PROPHECY—a database for high-resolution phenomics
• CYGD: the Comprehensive Yeast Genome Database
• The Candida Genome Database(CGD), a community resource for Candida al
• WormBase: a comprehensive data resource for Caenorhabditis biology and
• The Yeast Resource Center Public Data Repository
• Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resou
• EzCatDB: the Enzyme Catalytic-mechanism Database
• STRING: known and predicted protein–protein associations, integrated a
• SilkSatDb: a microsatellite database of the silkworm, Bombyx mori
• Reactome: a knowledgebase of biological pathways
• GeneNet in 2005
• Ensembl 2005
• DED: Database of Evolutionary Distances
• ChickVD: a sequence variation database for the chicken genome
• Improvements to GALA and dbERGE II: databases featuring genomic sequen
• The Vertebrate Genome Annotation(Vega) database
• The UCSC Proteome Browser
• Polymorphix: a sequence polymorphism database
• HCAD, closing the gap between breakpoints and genes
• DG-CST(Disease Gene Conserved Sequence Tags), a database of human–mou
• NCBI Reference Sequence(RefSeq): a curated non-redundant sequence dat
• L1Base: from functional annotation to prediction of active LINE-1 elem
• IPD—the Immuno Polymorphism Database
• FESD: a Functional Element SNPs Database in human
• Online Mendelian Inheritance in Man(OMIM), a knowledgebase of human g
• HAGR: the Human Ageing Genomic Resources
• Cancer gene expression database(CGED): a database for gene expression
• SNPeffect: a database mapping molecular phenotypic effects of human no
• ArrayExpress—a public repository for microarray gene expression data a
• MetaRouter: bioinformatics for bioremediation
• DynaProt 2D: an advanced proteomic database for dynamic online access
• The Stanford Microarray Database accommodates additional microarray pl
• SIEGE: Smoking Induced Epithelial Gene Expression Database
• AMPDB: the Arabidopsis Mitochondrial Protein Database
• Organelle DB: a cross-species database of protein localization and fun
• IMGT, the international ImMunoGeneTics information system?
• CR-EST: a resource for crop ESTs
• Oracle Database 10g: a platform for BLAST search and Regular Expressio
• VBASE2, an integrative V gene database
• BarleyBase—an expression profiling database for plant genomics
• MITOMAP: a human mitochondrial genome database—2004 update
• ASRP: the Arabidopsis Small RNA Project Database
• Arabidopsis nucleolar protein database(AtNoPDB)
• PlantMarkers—a database of predicted molecular markers from plants
• openSputnik—a database to ESTablish comparative plant genomics using u
• Rice Annotation Database(RAD): a contig-oriented database for map-bas
• RARGE: a large-scale database of RIKEN Arabidopsis resources ranging f
• GeneFarm, structural and functional annotation of Arabidopsis gene and
• PoMaMo—a comprehensive database for potato genome data
• The Legume Information System(LIS): an integrated information resourc
• Brassica ASTRA: an integrated database for Brassica genomic research
• Biomedical term mapping databases
• The PANTHER database of protein families, subfamilies, functions and p
• The Biomolecular Interaction Network Database and related tools 2005 u
• 3did: interacting protein domains of known three-dimensional structure
• Inparanoid: a comprehensive database of eukaryotic orthologs
• The Mouse Genome Database(MGD): from genes to mice—a community resour
• The Adaptive Evolution Database(TAED): a phylogeny based tool for com
• RatMap—rat genome tools and data
• The Rat Genome Database(RGD): developments towards a phenome database
• 5'SAGE: 5'-end Serial Analysis of Gene Expression database
• T1DBase, a community web-based resource for type 1 diabetes research
• The Human Anatomic Gene Expression Library(H-ANGEL), the H-Inv integr
• NCBI GEO: mining millions of expression profiles—database and tools
• GeneTide—Terra Incognita Discovery Endeavor: a new transcriptome focus
• Metagrowth: a new resource for the building of metabolic hypotheses in
• BacMap: an interactive picture atlas of annotated bacterial genomes
• Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae in
• EcoCyc: a comprehensive database resource for Escherichia coli
• EchoBASE: an integrated post-genomic database for Escherichia coli
• SilkDB: a knowledgebase for silkworm biology and genomics
• MDS_IES_DB: a database of macronuclear and micronuclear genes in spiro
• FlyBase: genes and gene models