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《核酸研究医学期刊》2004年第10期

editorial
the molecular biology database collection: 2004 update
genbank: update
the embl nucleotide sequence database
ddbj in the stream of various biological data
database resources of the national center for biotechnology information: update
mips: analysis and annotation of proteins from whole genomes
aclame: a classification of mobile genetic elements
imgt/geneinfo: enhancing v(d)j recombination database accessibility
islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their dna site specificities
xpro: database of eukaryotic protein-encoding genes
asd: the alternative splicing database
eased: extended alternatively spliced est database
dbtbs: database of transcriptional regulation in bacillus subtilis and its contribution to comparative genomics
dbtss, database of transcriptional start sites: progress report 2004
the eukaryotic promoter database epd: the impact of in silico primer extension
hemopdb: hematopoiesis promoter database, an information resource of transcriptional regulation in blood cell development
jaspar: an open-access database for eukaryotic transcription factor binding profiles
aptamer database
the european ribosomal rna database
the tmrna website: reductive evolution of tmrna in plastids and other endosymbionts
the microrna registry
pirsf: family classification system at the protein information resource
uniprot: the universal protein knowledgebase
protherm, version 4.0: thermodynamic database for proteins and mutants
dbsubloc: database of protein subcellular localization
thgs: a web-based database of transmembrane helices in genome sequences
the catalytic site atlas: a resource of catalytic sites and residues identified in enzymes using structural data
recent improvements to the prosite database
the pfam protein families database
smart 4.0: towards genomic data integration
esther, the database of the /?-hydrolase fold superfamily of proteins
eyesite: a semi-automated database of protein families in the eye
the knottin website and database: a new information system dedicated to the knottin scaffold
king: a database of protein kinases in genomes
merops: the peptidase database
update of nurebase: nuclear hormone receptor functional genomics
rpg: the ribosomal protein gene database
trsdb: a proteome database of transcription factors
aant: the amino acid
scor: structural classification of rna, version 2.0
archdb: automated protein loop classification as a tool for structural genomics
the astral compendium in 2004
domins: a web resource for domain insertions in known protein structures
the genomic threading database: a comprehensive resource for structural annotations of the genomes from key organisms
dsdbase: a consortium of native and modelled disulphide bonds in proteins
homstrad: recent developments of the homologous protein structure alignment database
imgt/3dstructure-db and imgt/structuralquery, a database and a tool for immunoglobulin, t cell receptor and mhc structural data
e-msd: an integrated data resource for bioinformatics
modbase, a database of annotated comparative protein structure models, and associated resources
the distribution and query systems of the rcsb protein data bank
scop database in 2004: refinements integrate structure and sequence family data
the swiss-model repository of annotated three-dimensional protein structure homology models
the superfamily database in 2004: additions and improvements
surface: a database of protein surface regions for functional annotation
3d-genomics: a database to compare structural and functional annotations of proteins between sequenced genomes
tops: an enhanced database of protein structural topology
genew: the human gene nomenclature database, 2004 updates
the gene ontology (go) database and informatics resource
the gene ontology annotation (goa) database: sharing knowledge in uniprot with gene ontology
the unified medical language system (umls): integrating biomedical terminology
deg: a database of essential genes
fusiondb: a database for in-depth analysis of prokaryotic gene fusion events
the kegg resource for deciphering the genome
the orfanage: an orfan database
transportdb: a relational database of cellular membrane transport systems
virgen: a comprehensive viral genome resource
the cybercell database (ccdb): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of escherichia coli
colibase: an online database for escherichia coli, shigella and salmonella comparative genomics
genprotec: an updated and improved analysis of functions of escherichia coli k-12 proteins
regulondb (version 4.0): transcriptional regulation, operon organization and growth conditions in escherichia coli k-12
molligen, a database dedicated to the comparative genomics of mollicutes
saccharomyces genome database (sgd) provides tools to identify and analyze sequences from saccharomyces cerevisiae and related sequences from other organisms
génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts
scmd: saccharomyces cerevisiae morphological database
ymgv: a cross-species expression data mining tool
apiest-db: analyzing clustered est data of the apicomplexan parasites
cryptodb: the cryptosporidium genome resource
dictybase: a new dictyostelium discoideum genome database
full-malaria 2004: an enlarged database for comparative studies of full-length cdnas of malaria parasites, plasmodium species
genedb: a resource for prokaryotic and eukaryotic organisms
tcruzidb: an integrated trypanosoma cruzi genome resource
flagdb++: a database for the functional analysis of the arabidopsis genome
phytoprot: a database of clusters of plant proteins
plantgdb, plant genome database and analysis tools
the tigr plant repeat databases: a collective resource for the identification of repetitive sequences in plants
tropgene-db, a multi-tropical crop information system
athamap: an online resource for in silico transcription factor binding sites in the arabidopsis thaliana genome
mips arabidopsis thaliana database (matdb): an integrated biological knowledge resource for plant genomics
bgi-ris: an integrated information resource and comparative analysis workbench for rice genomics
the rice pipeline: a unification tool for plant functional genomics
rice proteome database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003
maizegdb, the community database for maize genetics and genomics
sgmd: the soybean genomics and microarray database
cadre: the central aspergillus data repository
rnaidb and phenoblast: web tools for genome-wide phenotypic mapping projects
wormbase: a multi-species resource for nematode biology and genomics
flytrap, a database documenting a gfp protein-trap insertion screen in drosophila melanogaster
appadb: an acedb database for the nematode satellite organism pristionchus pacificus
nematode.net: a tool for navigating sequences from parasitic and free-living nematodes
nembase: a resource for parasitic nematode ests
brenda, the enzyme database: updates and major new developments
intenz, the integrated relational enzyme database
metacyc: a multiorganism database of metabolic pathways and enzymes
the amaze lightbench: a web interface to a relational database of cellular processes
the database of interacting proteins: 2004 update
intact: an open source molecular interaction database
stcdb: signal transduction classification database
mitop2, an integrated database on mitochondrial proteins in yeast and man
mitoproteome: mitochondrial protein sequence database and annotation system
ensembl 2004
frep: a database of functional repeats in mouse cdnas
the mouse genome database (mgd): integrating biology with the genome
the mouse sage site: database of public mouse sage libraries
pede (pig est data explorer): construction of a database for ests derived from porcine full-length cdna libraries
alugene: a database of alu elements incorporated within protein-coding genes
the ucsc table browser data retrieval tool
human protein reference database as a discovery resource for proteomics
huge: a database for human kiaa proteins, a 2004 update integrating hugeppi and rouge
lifedb: a database for functional genomics experiments integrating information from external sources, and serving as a sample tracking system
trome, trest and trgen: databases of predicted protein sequences
pathbase: a database of mutant mouse pathology
hgvbase: a curated resource describing human dna variation and phenotype relationships
toposnp: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association
rtcgd: retroviral tagged cancer gene database
snp500cancer: a public resource for sequence validation and assay development for genetic variation in candidate genes
ergdb: estrogen responsive genes database
improvements in the hbvar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies
cleanex: a database of heterogeneous gene expression data based on a consistent gene nomenclature
eico (expression-based imprint candidate organizer): finding disease-related imprinted genes
genepaint.org: an atlas of gene expression patterns in the mouse embryo
the centre for modeling human disease gene trap resource
germonline, a cross-species community knowledgebase on germ cell differentiation
the mouse gene expression database (gxd): updates and enhancements
hembase: browser and genome portal for hematology and erythroid biology
nascarrays: a repository for microarray data generated by nasc’s transcriptomics service
the pepr genechip data warehouse, and implementation of a dynamic time series query tool (sgqt) with graphical interface
gelbank: a database of annotated two-dimensional gel electrophoresis patterns of biological systems with completed genomes
antimic: a database of antimicrobial sequences
apd: the antimicrobial peptide database
the peptaibol database: a database for sequences and structures of naturally occurring peptaibols
orfdb: an information resource linking scientific content to a high-quality open reading frame (orf) collection
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