《核酸研究》.2006年.第Da期

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• A new generation of JASPAR, the open-access repository for transcripti
• TRANSFAC? and its module TRANSCompel?: transcriptional gene regulation
• TiProD: the Tissue-specific Promoter Database
• DBD: a transcription factor prediction database
• GRSDB: a database of quadruplex forming G-rich sequences in alternativ
• Argonaute—a database for gene regulation by mammalian microRNAs
• DBTSS: DataBase of Human Transcription Start Sites, progress report 20
• MulPSSM: a database of multiple position-specific scoring matrices of
• BIOZON: a hub of heterogeneous biological data
• EDITORIAL
• ISfinder: the reference centre for bacterial insertion sequences
• ABS: a database of Annotated regulatory Binding Sites from orthologous
• MPromDb: an integrated resource for annotation and visualization of ma
• SitesBase: a database for structure-based protein–ligand binding site
• SMART 5: domains in the context of genomes and networks
• The EROP-Moscow oligopeptide database
• OrthoMCL-DB: querying a comprehensive multi-species collection of orth
• PUMA2—grid-based high-throughput analysis of genomes and metabolic pat
• ODB: a database of operons accumulating known operons across multiple
• VIPERdb: a relational database for structural virology
• DPVweb: a comprehensive database of plant and fungal virus genes and g
• VMD: a community annotation database for oomycetes and microbial genom
• SIDDBASE: a database containing the stress-induced DNA duplex destabil
• Human protein reference database—2006 update
• Pfam: clans, web tools and services
• DMAPS: a database of multiple alignments for protein structures
• SIMAP: the similarity matrix of proteins
• MEROPS: the peptidase database
• LGICdb: a manually curated sequence database after the genomes
• MODBASE: a database of annotated comparative protein structure models
• Gene3D: modelling protein structure, function and evolution
• Nuclear Receptor Signaling Atlas(www.nursa.org): hyperlinking the nuc
• The PMDB Protein Model Database
• The RCSB PDB information portal for structural genomics
• The Database of Macromolecular Motions: new features added at the deca
• PANDIT: an evolution-centric database of protein and associated nucleo
• The SWISS-MODEL Repository: new features and functionalities
• The Gene Ontology(GO) project in 2006
• The integrated microbial genomes(IMG) system
• ChimerDB—a knowledgebase for fusion sequences
• DDBJ in preparation for overview of research activities behind data su
• The Molecular Biology Database Collection: 2006 update
• The imprinted gene and parent-of-origin effect database now includes p
• HUMHOT: a database of human meiotic recombination hot spots
• HOLLYWOOD: a comparative relational database of alternative splicing
• ASD: a bioinformatics resource on alternative splicing
• Transterm—extended search facilities and improved integration with oth
• cisRED: a database system for genome-scale computational discovery of
• ARED 3.0: the large and diverse AU-rich transcriptome
• MeRNA: a database of metal ion binding sites in RNA structures
• IRESite: the database of experimentally verified IRES structures(www.
• miRBase: microRNA sequences, targets and gene nomenclature
• miRNAMap: genomic maps of microRNA genes and their target genes in mam
• MODOMICS: a database of RNA modification pathways
• ShiBASE: an integrated database for comparative genomics of Shigella
• Génolevures complete genomes provide data and tools for comparative ge
• dictyBase, the model organism database for Dictyostelium discoideum
• The LIFEdb database in 2006
• MPact: the MIPS protein interaction resource on yeast
• TcruziDB: an integrated, post-genomics community resource for Trypanos
• The YEASTRACT database: a tool for the analysis of transcription regul
• Genome Snapshot: a new resource at the Saccharomyces Genome Database(
• Visualizing syntenic relationships among the hemiascomycetes with the
• CryptoDB: a Cryptosporidium bioinformatics resource update
• PINT: Protein–protein Interactions Thermodynamic Database
• iMOTdb—a comprehensive collection of spatially interacting motifs in p
• PPD v1.0—an integrated, web-accessible database of experimentally dete
• The REFOLD database: a tool for the optimization of protein expression
• E-MSD: improving data deposition and structure quality
• ProTherm and ProNIT: thermodynamic databases for proteins and protein–
• The PROSITE database
• NOPdb: Nucleolar Proteome Database
• LOCATE: a mouse protein subcellular localization database
• RegulonDB(version 5.0): Escherichia coli K-12 transcriptional regulat
• Megx.net—database resources for marine ecological genomics
• The UCSC Archaeal Genome Browser
• LEGER: knowledge database and visualization tool for comparative genom
• Phytophthora functional genomics database(PFGD): functional genomics
• PHI-base: a new database for pathogen host interactions
• FGDB: a comprehensive fungal genome resource on the plant pathogen Fus
• FLIGHT: database and tools for the integration and cross-correlation o
• WormBase: better software, richer content
• SGCEdb: a flexible database and web interface integrating experimental
• StellaBase: The Nematostella vectensis Genomics Database
• FlyRNAi: the Drosophila RNAi screening center database
• FlyBase: anatomical data, images and queries
• LMPD: LIPID MAPS proteome database
• Pathguide: a Pathway Resource List
• Tetrahymena Genome Database(TGD): a new genomic resource for Tetrahym
• AffinDB: a freely accessible database of affinities for protein–ligand
• The University of Minnesota Biocatalysis/Biodegradation Database: the
• MetaCyc: a multiorganism database of metabolic pathways and enzymes
• EndoNet: an information resource about endocrine networks
• TreeFam: a curated database of phylogenetic trees of animal gene famil
• The Mouse Functional Genome Database(MfunGD): functional annotation o
• OMIA(Online Mendelian Inheritance in Animals): an enhanced platform a
• The UCSC Genome Browser Database: update 2006
• QTL MatchMaker: a multi-species quantitative trait loci(QTL) database
• ITTACA: a new database for integrated tumor transcriptome array and cl
• HPtaa database-potential target genes for clinical diagnosis and immun
• CTGA: the database for genetic disorders in Arab populations
• BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-s
• DrugBank: a comprehensive resource for in silico drug discovery and ex
• ChloroplastDB: the Chloroplast Genome Database
• BioModels Database: a free, centralized database of curated, published
• RTPrimerDB: the real-time PCR primer and probe database, major update
• MitoP2: the mitochondrial proteome database—now including mouse data
• HvrBase++: a phylogenetic database for primate species
• GOBASE—a database of organelle and bacterial genome information
• Phytome: a platform for plant comparative genomics
• Gramene: a bird's eye view of cereal genomes
• DRASTIC—INSIGHTS: querying information in a plant gene expression data
• Plant MPSS databases: signature-based transcriptional resources for an
• xBASE, a collection of online databases for bacterial comparative geno
• ICDS database: interrupted CoDing sequences in prokaryotic genomes
• The Genomes On Line Database(GOLD) v.2: a monitor of genome projects
• SCOPPI: a structural classification of protein–protein interfaces
• The HUGO Gene Nomenclature Database, 2006 updates
• Flexible Structural Neighborhood—a database of protein structural simi
• From genomics to chemical genomics: new developments in KEGG
• INVHOGEN: a database of homologous invertebrate genes
• The Zebrafish Information Network: the zebrafish model organism databa
• dbPTM: an information repository of protein post-translational modific
• SNP500Cancer: a public resource for sequence validation, assay develop
• The International Gene Trap Consortium Website: a portal to all public
• EMAGE: a spatial database of gene expression patterns during mouse emb
• CAGE Basic/Analysis Databases: the CAGE resource for comprehensive pro
• AOBase: a database for antisense oligonucleotides selection and design
• PRIDE: a public repository of protein and peptide identifications for
• The PeptideAtlas project
• PepSeeker: a database of proteome peptide identifications for investig
• SuperNatural: a searchable database of available natural compounds
• GLIDA: GPCR-ligand database for chemical genomic drug discovery
• BioGRID: a general repository for interaction datasets
• pSTIING: a ‘systems’ approach towards integrating signalling pathways,
• The Mouse Genome Database(MGD): updates and enhancements
• Ensembl 2006
• DBTGR: a database of tunicate promoters and their regulatory elements
• TRANSPATH?: an information resource for storing and visualizing signal
• HTPSELEX—a database of high-throughput SELEX libraries for transcripti
• EMBL Nucleotide Sequence Database: developments in 2005
• EPD in its twentieth year: towards complete promoter coverage of selec
• GenBank
• snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box sn
• RNAi Codex: a portal/database for short-hairpin RNA(shRNA) gene-silen
• NPInter: the noncoding RNAs and protein related biomacromolecules inte
• TCDB: the Transporter Classification Database for membrane transport p
• Database resources of the National Center for Biotechnology Informatio
• MIPS: analysis and annotation of proteins from whole genomes in 2005
• The tmRDB and SRPDB resources
• The Universal Protein Resource(UniProt): an expanding universe of pro
• CyBase: a database of cyclic protein sequence and structure
• RMD: a rice mutant database for functional analysis of the rice genome
• The Rice Annotation Project Database(RAP-DB): hub for Oryza sativa ss
• OryGenesDB: a database for rice reverse genetics
• The Soybean Genome Database(SoyGD): a browser for display of duplicat
• Panzea: a database and resource for molecular and functional diversity
• mtDB: Human Mitochondrial Genome Database, a resource for population g
• IMGT/LIGM-DB, the IMGT? comprehensive database of immunoglobulin and T
• Epitome: database of structure-inferred antigenic epitopes
• The TIGR Maize Database
• Tomato Expression Database(TED): a suite of data presentation and ana