[转载]核酸数据库

1. Nucleotide Sequence Databases
1.1. International Nucleotide Sequence Database Collaboration
DDBJ—DNA Data Bank of Japan		All known nucleotide and protein sequences	http://www.ddbj.nig.ac.jp
EMBL Nucleotide Sequence Database		All known nucleotide and protein sequences	http://www.ebi.ac.uk/embl.html
GenBank?		All known nucleotide and protein sequences	http://www.ncbi.nlm.nih.gov/Entrez
1.2. Coding and coding DNA: genes, motifs and regulatory sites
ACLAME		A classification of genetic mobile elements	http://aclame.ulb.ac.be/
CORG		Comparative Regulatory Genomics: conserved non-coding blocks in vertebrate species	http://corg.molgen.mpg.de
CUTG		Codon Usage Tabulated from GenBank	http://www.kazusa.or.jp/codon/
ECRbase		Database of Evolutionary Conserved Regions, promoters, and transcription factor binding sites	http://ecrbase.dcode.org/
Entrez Gene		Gene-centered information at NCBI	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
FESD		Functional Element SNPs Database: SNPs located within promoters, UTRs, etc., of human genes	http://sysbio.kribb.re.kr/FESD/
FREP		Functional Repeats in mouse cDNAs	http://facts.gsc.riken.go.jp/FREP/
Genetic Codes		Genetic codes in various organisms and organelles	http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c
GISSD		Group I Intron Sequence and Structure Database	http://www.rna.whu.edu.cn/gissd
GyDB		Gypsy database of mobile genetic elements	http://gydb.uv.es/gydb/intro.htm
HumHot		Human meiotic recombination hot spots	http://www.jncasr.ac.in/humhot/
InSatDb		Sequences and properties of insect microsatellites	http://www.cdfd.org.in/insatdb
ISfinder		Insertion sequences from bacteria and archaea	http://www-is.biotoul.fr
Islander		Pathogenicity islands and prophages in bacterial genomes	http://www.indiana.edu/~islander
L1Base		Functional annotation and prediction of LINE-1 elements	http://line1.molgen.mpg.de
MethDB		DNA methylation data, patterns and profiles	http://www.methdb.de
MICdb		Prokaryotic microsatellites	http://210.212.212.7/MIC/index.html
NPRD		Nucleosome Positioning Region Database	http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz?page+ LibInfo+-id+2Xnp11RCiPU+-lib+NUCLEOSOME
OriDB		DNA Replication Origin Database: Confirmed and predicted sites	http://www.oridb.org/
PACRAT		Archaeal and bacterial intergenic sequence features	No longer maintained
PANDIT		Protein and associated nucleotide domains with inferred trees	http://www.ebi.ac.uk/goldman-srv/pandit/
Patome		Annotated sequences from patents and patent applications	http://www.patome.org
PolymiRTS		Polymorphism in microRNA Target Site	http://compbio.utmem.edu/miRSNP/
PseudoGene.org		Pseudogenes in eukaryotic and prokaryotic genomes	http://www.pseudogene.org/
RECODE		Genes using programmed translational recoding in their expression	http://recode.genetics.utah.edu
RefSeq		Reference Sequence database: an integrated, non-redundant set of genomic DNA, RNA, and protein sequences	http://www.ncbi.nlm.nih.gov/RefSeq/
RetrOryza		LTR-retrotransposons in rice	http://www.retroryza.org
S/MARt DB		Nuclear scaffold/matrix attached regions	http://smartdb.bioinf.med.uni-goettingen.de/
SNPSTR		Microsatellite compound markers in 5 vertebrate genomes	http://www3.imperial.ac.uk/theoreticalgenomics/data-software
STRBase		Short tandem DNA repeats database	http://www.cstl.nist.gov/div831/strbase/
Synthetic Gene DB		Synthetic genes described in peer-reviewed literature	http://www.evolvingcode.net/codon/sgdb/index.php
TIGR plant repeat DB		Classification of repetitive sequences in plant genomes	http://www.tigr.org/tdb/e2k1/plant.repeats
TranspoGene		Transposed elements influence on the transcriptome of seven vertebrates and invertebrates	http://transpogene.tau.ac.il/
TRDB		Tandem repeats in genomic DNA	http://tandem.bu.edu/cgi-bin/trdb/trdb.exe
UgMicroSatdb		UniGene MicroSatellite database: short tandem repeats from various eukaryotic genomes	http://ipu.ac.in/usbt/UgMicroSatdb.htm
UniVec		Vector sequences, adapters, linkers and primers used in DNA cloning, used to check for vector contamination	http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html
UTRdb/UTRsite		5'- and 3'-UTRs of eukaryotic mRNAs	http://bighost.area.ba.cnr.it/BIG/UTRHome/
UTRome		3'UTRs and their functional elements in C. elegans	http://www.utrome.org
Vectordb		Characterization and classification of nucleic acid vectors	http://seq.yeastgenome.org/vectordb/
VISTA Enhancer Browser		Enhancer elements in the human genome	http://enhancer.lbl.gov/
1.3. Gene structure, introns and exons, splice sites
ASAP II		Comparative analysis of alternative splicing in animal species	http://bioinfo.mbi.ucla.edu/ASAP2/
ASDB		Alternative Splicing Database: protein products and expression patterns of alternatively-spliced genes	http://hazelton.lbl.gov/~teplitski/alt/
ASHESdb		Alternatively Spliced Human genes by Exon Skipping	http://sege.ntu.edu.sg/wester/ashes/
ASTD		Alternative Splicing and Transcript Diversity database	http://www.ebi.ac.uk/astd/
ATD		Alternate transcript diversity database	Superseded by ASTD, no. 28
ChimerDB		Chimeric (fusion) sequences in human, rat and mouse	http://genome.ewha.ac.kr/ChimerDB/
EASED		Extended Alternatively Spliced EST Database	http://eased.bioinf.mdc-berlin.de/
ECgene		Genome annotation for alternative splicing	http://genome.ewha.ac.kr/ECgene/
EDAS		EST-derived alternative splicing database	http://www.ig-msk.ru:8005/EDAS/
EID		Exon-intron database	http://www.meduohio.edu/bioinfo/eid/
ExInt		Exon–intron structure of eukaryotic genes	http://sege.ntu.edu.sg/wester/exint/
ExtraTRAIN		Extragenic regions and transcriptional regulators in bacteria and archaea	http://www.era7.com/ExtraTrain/
FUGOID		Functional genomics of organelle introns database	http://web.austin.utexas.edu/fugoid/introndata/main.htm
H-DBAS		Human database of alternative splicing	http://jbirc.jbic.or.jp/h-dbas/
Hollywood		Exon annotation database	http://hollywood.mit.edu
HS3D		Homo Sapiens Splice Sites Dataset	http://www.sci.unisannio.it/docenti/rampone/
Intronerator		Alternative splicing in C. elegans and C. briggsae	http://hgwdev-hiram.cse.ucsc.edu/IntronWS120/
ProSAS		Protein Structure and Alternative Splicing: effects of alternative splicing events on protein structure	http://services.bio.ifi.lmu.de/ProSAS
SpliceDB		Canonical and non-canonical mammalian splice sites	http://www.softberry.com/berry.phtml?topic=splicedb&group=data&subgroup=spldb
SpliceInfo		Modes of alternative splicing in human genome	http://spliceinfo.mbc.nctu.edu.tw/
SpliceNest		Visualizing Splicing of Genes from EST Data	http://splicenest.molgen.mpg.de/
TassDB		Tandem Splice Site Database	http://helios.informatik.uni-freiburg.de/TassDB/
U12DB		Database of orthologous U12-type spliceosomal introns	http://genome.imim.es/cgi-bin/u12db/u12db.cgi
Xpro		Eukaryotic protein-encoding DNA sequences, both intron-containing and intron-less genes	http://origin.bic.nus.edu.sg/xpro/
Yeast Intron Database		Ares lab database of splicesomal introns in S. cerevisiae	http://www.cse.ucsc.edu/research/compbio/yeast_introns.html
1.4. Transcriptional regulator sites and transcription factors
ABS	Annotated regulatory binding sites from orthologous promoters		http://genome.imim.es/datasets/abs2005/
ACTIVITY	Functional DNA/RNA site activity		http://wwwmgs.bionet.nsc.ru/mgs/systems/activity/
ASPD	Artificial selected proteins/peptides database		http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/
CisRed	Human regulatory DNA sequence motifs		http://www.cisred.org/
CMGSDB	Computational models for gene silencing in C. elegans		https://bioinformatics.cs.vt.edu/cmgs/CMGSDB/
COXPRESdb	Coexpressed genes and networks in human and mouse		http://coxpresdb.hgc.jp/
CTCF Binding Site DB	Experimentally identified and predicted CTCF binding sties		http://insulatordb.utmem.edu/
DBD	Transcription factor prediction database		http://www.transcriptionfactor.org/
DBTBS	Bacillus subtilis promoters and transcription factors		http://dbtbs.hgc.jp/
DBTSS	Database of transcriptional start sites		http://dbtss.hgc.jp/
DoOP	Databases of Orthologous Promoters: chordates and plants		http://doop.abc.hu/
DPInteract	Binding sites for E. coli DNA-binding proteins		http://arep.med.harvard.edu/dpinteract/
EPD	Eukaryotic promoter database		http://www.epd.isb-sib.ch/
GeneNet	Database on gene network components		http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet/
GenomeTraFaC	Conserved regulatory elements of human and mouse genes		http://genometrafac.cchmc.org
HTPSELEX	Transcription factor binding site sequences obtained using high-throughput SELEX method		http://www.isrec.isb-sib.ch/htpselex/
JASPAR	PSSMs for transcription factor DNA-binding sites		http://jaspar.cgb.ki.se
MAPPER	Putative transcription factor binding sites in various genomes		http://bio.chip.org/mapper
MPromDB	Mammalian promoter database		http://bioinformatics.med.ohio-state.edu/MPromDb
ODB	Operon database		http://odb.kuicr.kyoto-u.ac.jp/
ooTFD	Object-oriented transcription factors database		http://www.ifti.org/ootfd
ORegAnno	Open REGulatory ANNOtation database		http://www.oreganno.org/
Osteo-Promoter DB	Genes in osteogenic proliferation and differentiation		http://www.opd.tau.ac.il
PLACE	Plant cis-acting regulatory DNA elements		http://www.dna.affrc.go.jp/PLACE/
PlantCARE	Plant promoters and cis-acting regulatory elements		http://bioinformatics.psb.ugent.be/webtools/plantcare/html/
PlantProm	Plant promoter sequences for RNA polymerase II		http://mendel.cs.rhul.ac.uk/mendel.php?topic=plantprom
PlantTFDB	Plant Transcription Factor Database		http://planttfdb.cbi.pku.edu.cn
PReMod	Predicted transcriptional regulatory modules in the human genome		http://genomequebec.mcgill.ca/PReMod
PRODORIC	Prokaryotic database of gene regulation networks		http://prodoric.tu-bs.de/
PromEC	E. coli promoters with experimentally-identified transcriptional start sites		http://margalit.huji.ac.il/promec/
ProTISA	Translation Initiation Site Annotation in prokaryotic genomes		http://mech.ctb.pku.edu.cn/protisa/
RegulonDB	Transcriptional regulation and operon organization in E.coli		http://regulondb.ccg.unam.mx/
rSNP Guide	SNPs in regulatory gene regions		http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/
SCPD	Saccharomyces cerevisiae promoter database		http://rulai.cshl.edu/SCPD/
SELEXdb	Selected DNA/RNA functional site sequences		http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/
SwissRegulon database	Genome-wide annotations of regulatory sites in the intergenic regions		http://www.swissregulon.unibas.ch
TESS	Transcription element search system		http://www.cbil.upenn.edu/tess
TiProD	Tissue-specific promoter database		http://tiprod.cbi.pku.edu.cn:8080/index.html
Tractor_DB	Transcription factors in gamma-proteobacteria database		http://www.tractor.lncc.br
TRANSCompel?	Transcriptional regulation, composite regulatory elements		http://www.gene-regulation.com/pub/ databases.html#transcompel
TRANSFAC?	Transcription factors, gene regulation, positional weight matrices		http://www.gene-regulation.com
TransfactomeDB	Nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors		http://bussemakerlab.org/YeastTransfactomeDB/
TRANSPATH	Signal transduction pathways, vizualization and expression data analysis		http://www.biobase.de/pages/products/databases.html
Transterm	Codon usage, start and stop signals		http://guinevere.otago.ac.nz/transterm.html
TRED	Transcriptional regulatory element database		http://rulai.cshl.edu/tred
TRRD	Transcription regulatory regions of eukaryotic genes		http://www.bionet.nsc.ru/trrd/
TrSDB	Transcription factor database		http://bioinf.uab.es/cgi-bin/trsdb/trsdb.pl
YEASTRACT	Yeast transcriptional regulation		http://www.yeastract.com

 

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