［推荐］ 2004 Molecular Biology Databas of NAR

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148
个数据库的整理已全部完成！感谢在这个过程中，大力支持我们的所有战友，希望大家继续支持本版工作。

-- Biozy，imsupergene

imsupergene last update
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大家一看就明白 :) http://nar.oupjournals.org/content/vol32/suppl_1
欢迎大家随时来查询/使用/转载我们收集的数据库信息(帖子)！
这样我们的付出才有了意义，帖子本身也会有高的“影响因子”！

但转载时请注明"丁香园-生物信息学讨论版"!多谢!
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NAR做的数据库分类：Database Categories List
Genomics Databases (non-vertebrate)
Human and other Vertebrate Genomes
Human Genes and Diseases
Metabolic and Signaling Pathways
Microarray Data and other Gene Expression Databases
Nucleotide Sequence Databases
Other Molecular Biology Databases
Protein sequence databases
Proteomics Resources
RNA sequence databases
Structure Databases
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总共收录：143个数据库
总目录： http://www.dxy.cn/bbs/post/view?bid=73&id=610909

新年送分 数据库整理 每个数据库1-3分!
格式要求:
[Database] database name
[Institute]
[Address]
[URL] http://www.dxy.cn/bbs/
[Abstract]:
[中文简介]:
可以基于abstract点处最重要的几点就可以！就是两三句话说出该数据库的特色！让大家一看就知道！
[Comments]:
你的评价或和你所知道的相关的数据库比较！(可选择)

必读：
为避免重复劳动，请大家发文前看看是否已经有人发过了,重复者原则上不给与加分!介绍过于简单者暂时不给加分！
已完成的数据库列表下边或这里!




目前已经完成列表：供大家参阅：蓝色表示已经完成! (y)
Update Time： 2004-03-14 9:35 by imsupergene

注意：此更新不包括已经被参与冲刺的战友所承包的部分，具体请参见
http://www.dxy.cn/bbs/post/view?bid=73&id=789129&sty=1&tpg=1&age=0


1 The Molecular Biology Database Collection: 2004 update
2 GenBank: update
3 The EMBL Nucleotide Sequence Database
4 DDBJ in the stream of various biological data
5 Database resources of the National Center for Biotechnology Information: update
6 MIPS: analysis and annotation of proteins from whole genomes
7 ACLAME: A CLAssification of Mobile genetic Elements
8 HERVd: the Human Endogenous RetroViruses Database: update
9 IMGT/GeneInfo: enhancing V(D)J recombination database accessibility
10 Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities
11 Xpro: database of eukaryotic protein-encoding genes
12 ASD: the Alternative Splicing Database
13 EASED: Extended Alternatively Spliced EST Database
14 DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics
15 DBTSS, DataBase of Transcriptional Start Sites: progress report 2004
16 The Eukaryotic Promoter Database EPD: the impact of in silico primer extension
17 HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development
18 JASPAR: an open-access database for eukaryotic transcription factor binding profiles
19 Aptamer Database
20 The European ribosomal RNA database
21 The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts
22 The microRNA Registry
23 PIRSF: family classification system at the Protein Information Resource
24 UniProt: the Universal Protein knowledgebase
25 ProTherm, version 4.0: thermodynamic database for proteins and mutants
26 DBSubLoc: database of protein subcellular localization
27 THGS: a web-based database of Transmembrane Helices in Genome Sequences
28 The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data
29 Recent improvements to the PROSITE database
30 The Pfam protein families database
31 SMART 4.0: towards genomic data integration
32 ESTHER, the database of the α/β-hydrolase fold superfamily of proteins
33 EyeSite: a semi-automated database of protein families in the eye
34 KinG: a database of protein kinases in genomes
35 The KNOTTIN website and database: a new information system dedicated to the knottin scaffold
36 MEROPS: the peptidase database
37 Update of NUREBASE: nuclear hormone receptor functional genomics
38 RPG: the Ribosomal Protein Gene database
39 TrSDB: a proteome database of transcription factors
40 AANT: the Amino Acid–Nucleotide Interaction Database
41 SCOR: Structural Classification of RNA, version 2.0
42 ArchDB: automated protein loop classification as a tool for structural genomics
43 The ASTRAL Compendium in 2004
44 DomIns: a web resource for domain insertions in known protein structures
45 The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms
46 DSDBASE: a consortium of native and modelled disulphide bonds in proteins
47 HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database
48 IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data
49 E-MSD: an integrated data resource for bioinformatics
50 MODBASE, a database of annotated comparative protein structure models, and associated resources
51 The distribution and query systems of the RCSB Protein Data Bank
52 SCOP database in 2004: refinements integrate structure and sequence family data
53 The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models
54 The SUPERFAMILY database in 2004: additions and improvements
55 SURFACE: a database of protein surface regions for functional annotation
56 3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes
57 TOPS: an enhanced database of protein structural topology
58 Genew: the Human Gene Nomenclature Database, 2004 updates
59 The Gene Ontology (GO) database and informatics resource
60 The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology
61 The Unified Medical Language System (UMLS): integrating biomedical terminology
62 DEG: a database of essential genes
63 FusionDB: a database for in-depth analysis of prokaryotic gene fusion events
64 The KEGG resource for deciphering the genome
65 The ORFanage: an ORFan database
66 TransportDB: a relational database of cellular membrane transport systems
67 VirGen: a comprehensive viral genome resource
68 The CyberCell Database (CCD: a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli
69 coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics
70 GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins
71 RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12
73 MolliGen, a database dedicated to the comparative genomics of Mollicutes
74 Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms
75 Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts
76 SCMD: Saccharomyces cerevisiae Morphological Database
77 yMGV: a cross-species expression data mining tool
78 ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites
79 CryptoDB: the Cryptosporidium genome resource
80 dictyBase: a new Dictyostelium discoideum genome database
81 Full-malaria 2004: an enlarged database for comparative studies of full-length cDNAs of malaria parasites, Plasmodium species
82 GeneDB: a resource for prokaryotic and eukaryotic organisms
83 TcruziDB: an integrated Trypanosoma cruzi genome resource
84 FLAGdb++: a database for the functional analysis of the Arabidopsis genome
85 PHYTOPROT: a database of clusters of plant proteins
86 PlantGDB, plant genome database and analysis tools
87 The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants
88 TropGENE-DB, a multi-tropical crop information system
89 AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome
90 MIPS Arabidopsis thaliana Database (MAtD: an integrated biological knowledge resource for plant genomics
91 BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics
92 The Rice PIPELINE: a unification tool for plant functional genomics
93 Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003
94 MaizeGDB, the community database for maize genetics and genomics
95 SGMD: the Soybean Genomics and Microarray Database
96 CADRE: the Central Aspergillus Data REpository
97 RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects
98 WormBase: a multi-species resource for nematode biology and genomics
99 Flytrap, a database documenting a GFP protein-trap insertion screen in Drosophila melanogaster
100 AppaDB: an AcedB database for the nematode satellite organism Pristionchus pacificus
101 Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes
102 NEMBASE: a resource for parasitic nematode ESTs
103 BRENDA, the enzyme database: updates and major new developments
104 IntEnz, the integrated relational enzyme database
105 MetaCyc: a multiorganism database of metabolic pathways and enzymes
106 The aMAZE LightBench: a web interface to a relational database of cellular processes
107 The Database of Interacting Proteins: 2004 update
108 IntAct: an open source molecular interaction database
109 STCDB: Signal Transduction Classification Database
110 MitoP2, an integrated database on mitochondrial proteins in yeast and man
111 MitoProteome: mitochondrial protein sequence database and annotation system
112 Ensembl 2004
113 FREP: a database of functional repeats in mouse cDNAs
114 The Mouse Genome Database (MGD): integrating biology with the genome
115 The Mouse SAGE Site: database of public mouse SAGE libraries
116 PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries
117 AluGene: a database of Alu elements incorporated within protein-coding genes
118 The UCSC Table Browser data retrieval tool
119 Human protein reference database as a discovery resource for proteomics
120 HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE
121 LIFEdb: a database for functional genomics experiments integrating information from external sources, and serving as a sample tracking system
122 trome, trEST and trGEN: databases of predicted protein sequences
123 Pathbase: a database of mutant mouse pathology
124 HGVbase: a curated resource describing human DNA variation and phenotype relationships
125 topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association
126 RTCGD: retroviral tagged cancer gene database
127 SNP500Cancer: a public resource for sequence validation and assay development for genetic variation in candidate genes
128 ERGDB: Estrogen Responsive Genes Database
129 Improvements in the HbVar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies
130 CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature
131 EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes
132 GenePaint.org: an atlas of gene expression patterns in the mouse embryo
133 The Centre for Modeling Human Disease Gene Trap resource
134 GermOnline, a cross-species community knowledgebase on germ cell differentiation
135 The mouse Gene Expression Database (GXD): updates and enhancements
136 Hembase: browser and genome portal for hematology and erythroid biology
137 NASCArrays: a repository for microarray data generated by NASC’s transcriptomics service
138 The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface
139 GELBANK: a database of annotated two-dimensional gel electrophoresis patterns of biological systems with completed genomes
140 ANTIMIC: a database of antimicrobial sequences
141 APD: the Antimicrobial Peptide Database
142 The Peptaibol Database: a database for sequences and structures of naturally occurring peptaibols
143 ORFDB: an information resource linking scientific content to a high-quality Open Reading Frame (ORF) collection

增补5个数据库：
144 SWISS-2DPAGE：Two-dimensional polyacrylamide gel electrophoresis database
145 PAD - Proteome Analysis Database
146 AAindex is a database of amino acid indices and amino acid mutation matrices
147 PEP: Predictions for Entire Proteomes
148 RESID