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《核酸研究医学期刊》
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《核酸研究医学期刊》2005年第24期

editorial
the molecular biology database collection: 2005 update
ddbj in collaboration with mass-sequencing teams on annotation
the embl nucleotide sequence database
genbank
database resources of the national center for biotechnology information
the european bioinformatics institute's data resources: towards systems biology
entrez gene: gene-centered information at ncbi
hoppsigen: a database of human and mouse processed pseudogenes
nprd: nucleosome positioning region database
the tigr gene indices: clustering and assembling est and known genes and integration with eukaryotic genomes
ecgene: genome annotation for alternative splicing
spliceinfo: an information repository for mrna alternative splicing in human genome
doop: databases of orthologous promoters, collections of clusters of orthologous upstream sequences from chordates and plants
the mapper database: a multi-genome catalog of putative transcription factor binding sites
tractor_db: a database of regulatory networks in gamma-proteobacterial genomes
tred: a transcriptional regulatory element database and a platform for in silico gene regulation studies
husida―the human sirna database: an open-access database for published functional sirna sequences and technical details of efficient transfer into recipient cells
noncode: an integrated knowledge database of non-coding rnas
rfam: annotating non-coding rnas in complete genomes
rnadb―a comprehensive mammalian noncoding rna database
sirnadb: a database of sirna sequences
the small subunit rrna modification database
compilation of trna sequences and sequences of trna genes
utrdb and utrsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mrnas
pa-gosub: a searchable database of model organism protein sequences with their predicted gene ontology molecular function and subcellular localization
the universal protein resource (uniprot)
nmpdb: database of nuclear matrix proteins
psortdb: a protein subcellular localization database for bacteria
spd―a web-based secreted protein database
tpmd: a database and resources of microsatellite marker genotyped in taiwanese populations
eblocks: enumerating conserved protein blocks to achieve maximal sensitivity and specificity
pdbsite: a database of the 3d structure of protein functional sites
adda: a domain database with global coverage of the protein universe
cdd: a conserved domain database for protein classification
funshift: a database of function shift analysis on protein subfamilies
interpro, progress and status in 2005
precise: a database of predicted and consensus interaction sites in enzymes
the prodom database of protein domain families: more emphasis on 3d
protonet 4.0: a hierarchical classification of one million protein sequences
s4: structure-based sequence alignments of scop superfamilies
the sbase domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines
the systers protein family database in 2005
rebase―restriction enzymes and dna methyltransferases
the rcsb protein data bank: a redesigned query system and relational database based on the mmcif schema
pdb-ligand: a ligand database based on pdb for the automated and customized classification of ligand-binding structures
carbohydrate structure suite (css): analysis of carbohydrate 3d structures derived from the pdb
the cath domain structure database and related resources gene3d and dhs provide comprehensive domain family information for genome analysis
gendis: genomic distribution of protein structural domain superfamilies
imgt/gene-db: a comprehensive database for human and mouse immunoglobulin and t cell receptor genes
e-msd: an integrated data resource for bioinformatics
pdbsum more: new summaries and analyses of the known 3d structures of proteins and nucleic acids
sting report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the sting database
pdb_tm: selection and membrane localization of transmembrane proteins in the protein data bank
pfd: a database for the investigation of protein folding kinetics and stability
the panther database of protein families, subfamilies, functions and pathways
biomedical term mapping databases
the ribosomal database project (rdp-ii): sequences and tools for high-throughput rrna analysis
partigenedb―collating partial genomes
the pedant genome database in 2005
poxvirus bioinformatics resource center: a comprehensive poxviridae informational and analytical resource
bacmap: an interactive picture atlas of annotated bacterial genomes
metagrowth: a new resource for the building of metabolic hypotheses in microbiology
vfdb: a reference database for bacterial virulence factors
echobase: an integrated post-genomic database for escherichia coli
ecocyc: a comprehensive database resource for escherichia coli
pseudomonas aeruginosa genome database and pseudocap: facilitating community-based, continually updated, genome annotation
the diatom est database
the ashbya genome database (agd)―a tool for the yeast community and genome biologists
candidadb: a genome database for candida albicans pathogenomics
the candida genome database (cgd), a community resource for candida albicans gene and protein information
cygd: the comprehensive yeast genome database
prophecy―a database for high-resolution phenomics
fungal blast and model organism blastp best hits: new comparison resources at the saccharomyces genome database (sgd)
the yeast resource center public data repository
wormbase: a comprehensive data resource for caenorhabditis biology and genomics
flybase: genes and gene models
mds_ies_db: a database of macronuclear and micronuclear genes in spirotrichous ciliates
silkdb: a knowledgebase for silkworm biology and genomics
ezcatdb: the enzyme catalytic-mechanism database
3did: interacting protein domains of known three-dimensional structure
the biomolecular interaction network database and related tools 2005 update
genenet in 2005
reactome: a knowledgebase of biological pathways
silksatdb: a microsatellite database of the silkworm, bombyx mori
string: known and predicted protein
chickvd: a sequence variation database for the chicken genome
ded: database of evolutionary distances
ensembl 2005
the ucsc proteome browser
the vertebrate genome annotation (vega) database
improvements to gala and dberge ii: databases featuring genomic sequence alignment, annotation and experimental results
the mouse genome database (mgd): from genes to mice―a community resource for mouse biology
inparanoid: a comprehensive database of eukaryotic orthologs
polymorphix: a sequence polymorphism database
the rat genome database (rgd): developments towards a phenome database
ratmap―rat genome tools and data
the adaptive evolution database (taed): a phylogeny based tool for comparative genomics
l1base: from functional annotation to prediction of active line-1 elements
ncbi reference sequence (refseq): a curated non-redundant sequence database of genomes, transcripts and proteins
dg-cst (disease gene conserved sequence tags), a database of human
hcad, closing the gap between breakpoints and genes
online mendelian inheritance in man (omim), a knowledgebase of human genes and genetic disorders
fesd: a functional element snps database in human
ipd―the immuno polymorphism database
snpeffect: a database mapping molecular phenotypic effects of human non-synonymous coding snps
cancer gene expression database (cged): a database for gene expression profiling with accompanying clinical information of human cancer tissues
hagr: the human ageing genomic resources
t1dbase, a community web-based resource for type 1 diabetes research
5'sage: 5'-end serial analysis of gene expression database
arrayexpress―a public repository for microarray gene expression data at the ebi
genetide―terra incognita discovery endeavor: a new transcriptome focused member of the genecards/genenote suite of databases
ncbi geo: mining millions of expression profiles―database and tools
the human anatomic gene expression library (h-angel), the h-inv integrative display of human gene expression across disparate technologies and platforms
siege: smoking induced epithelial gene expression database
the stanford microarray database accommodates additional microarray platforms and data formats
dynaprot 2d: an advanced proteomic database for dynamic online access to proteomes and two-dimensional electrophoresis gels
metarouter: bioinformatics for bioremediation
imgt, the international immunogenetics information system?
organelle db: a cross-species database of protein localization and function
ampdb: the arabidopsis mitochondrial protein database
mitomap: a human mitochondrial genome database―2004 update
barleybase―an expression profiling database for plant genomics
cr-est: a resource for crop ests
opensputnik―a database to establish comparative plant genomics using unsaturated sequence collections
plantmarkers―a database of predicted molecular markers from plants
arabidopsis nucleolar protein database (atnopdb)
asrp: the arabidopsis small rna project database
genefarm, structural and functional annotation of arabidopsis gene and protein families by a network of experts
rarge: a large-scale database of riken arabidopsis resources ranging from transcriptome to phenome
rice annotation database (rad): a contig-oriented database for map-based rice genomics
brassica astra: an integrated database for brassica genomic research
the legume information system (lis): an integrated information resource for comparative legume biology
pomamo―a comprehensive database for potato genome data
vbase2, an integrative v gene database
oracle database 10g: a platform for blast search and regular expression pattern matching in life sciences
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