RNA Regulation
deepBase
fRNADB: FUNCTIONAL RNA DATABASE
GENE-SPECIFIC siRNA SELECTOR
INSERT DESIGN TOOL (AMBION)
NPInter
RegRNA: REGULATORY RNA MOTIFS AND ELEMENTS FINDER
RibEx: RIBOSWITCH EXPLORER
RiDDLE
RNAdb
RNAi CONSORTIUM shRNA LIBRAY
RNAi DESIGN (INTEGRATED DNA TECHNOLOGIES)
RNAi EXPLORER™
RNAmutants
siDESIGN® CENTER (DHARMACON)
siDIRECT
siRNA AT WHITEHEAD
siRNA DESIGN
siRNA TARGET FINDER (AMBION)
TROD: T7 RNAi OLIGO DESIGNER)
Sequence Alignment
4SALE: RNA SEQUENCE ALIGNMENT AND EDITING
3D-FOOTPRINT
3DNALandscapes
ACT: ARTEMIS COMPARISON TOOL
bl2BLAST: BLAST 2 SEQUENCES
BLink:BLAST LINK (NCBI)
CENSOR
CIRCOS
CORRELOGO
DIALIGN 2
ECR BROWSER
GALAXY
GALAXY SCREENCASTS
GeneCoder
HOMOLOGENE
InterPro
MEME/MAST
MODEL MAKER (NCBI)
NNDB: NEAREST NEIGHBOR DATABASE
OrthoSelect
PACDB: SEARCH BY GENOME ALIGNMENT
PARALIGN
PIPMAKER: PERCENT IDENTITY PLOT
REPEATMASKER
RevTrans
RU: REPBASE UPDATE
SERpredict
SIB BLAST SERVER: SIMPLE IS BEAUTIFUL
SPIDEY
SPLIGN (NCBI)
WAVIS: ALIGNMENT VISUALIZATION TOOLS
WebGMAP
Wise2
zPICTURE
Sequence Retrieval
CENSOR
DDBJ: DNA DATA BANK OF JAPAN
DNA PATENT DATABASE
EMBL DOCUMENTATION
ENTREZ GENE (NCBI)
ENTREZ GLOBAL QUERY
ENTREZ: ACCESS TO NCBI DATABASES
FASTA/SSEARCH/GGSEARCH/GLSEARCH
FRAME-PROFILESCAN SERVER
GENBANK®
GENECARDS®
GENOMENET
INTERNATIONAL NUCLEOTIDE SEQUENCE DATABASE COLLABORATION
NCBI SITE MAP
NCBI: NATIONAL CENTER FOR BIOTECHNOLOGY INFORMATION
PATOME DB: DATABASE OF ISSUED AND PUBLISHED BIOLOGICAL SEQUENCES
SEQUIN
SRS@EMBL-EBI
TELOMERASE DATABASE
Transcription factors and bindning sites
AGRIS: ARABIDOPSIS GENE REGULATORY INFORMATION SERVER
AthaMap
CEAS: CIS-REGULATORY ELEMENT ANNOTATION SYSTEM
CisMols ANALYZER: Cis- REGULATORY MODULES
cisRED: GENOME-WIDE REGULATORY MODULE AND ELEMENT PREDICTIONS
CLUSTER BUSTER
CONREAL: CONSERVED REGULATORY ELEMENTS ANCHORED ALIGNMENT
CONSITE
DATF: DATABASE OF Arabidopsis TRANSCRIPTION FACTORS
DBD: TRANSCRIPTION FACTOR PREDICTION DATABASE
DiRE: DISTANT REGULATORY ELEMENTS OF CO-REGULATED GENES
HOMEOBOX PAGE
HOMEODOMAIN RESOURCE
HOX-PRO
HTPSELEX DATABASE
INCLUSive
JASPAR
jPREdictor
MAPPER
MATBASE
MATINSPECTOR
MoD: MOTIF DISCOVERY
MOTIFVIZ
ORegAnno: OPEN REGULATORY ANNOTATION DATABASE
PAZAR
PLACE: PLANT CIS-ACTING REGULATORY DNA ELEMENTS
ProteDNA
RSAT: REGULATORY SEQUENCE ANALYSIS TOOLS
rVISTA
SeqVISTA
TARGET EXPLORER
TESS: TRANSCRIPTION ELEMENT SEARCH SYSTEM
TFBScluster
TFSEARCH
TOUCAN 2
TRACTOR DB
TRANSCompel®
TRANSFAC®
TRANSPATH®
TRANSTERM
TRAWLER
TRED: TRANSCRIPTIONAL REGULATORY ELEMENT DATABASE
TrSDB
VOMBAT
YMF
ZINC FINGER TOOLS
Transcription Promoter Sites
ANNOTATIONS (OF TRANSCRIPTION FACTOR BINDING SITES WITHIN ORTHOLOGOUS PROMOTERS)
BKL Transfac®
ChromDB
CMA: COMPOSITE MODULE ANALYST
COREPROMOTER FINDER (CSHL)
CREB TARGET GENE DATABASE
CSHLmpd: COLD SPRING HARBOR LABORATORY MAMMALIAN PROMOTER DATABASE
dbQSNP
DBTSS: DATABASE OF TRANSCRIPTION START SITES
EPD: EUKARYOTIC PROMOTER DATABASE
GENE2PROMOTER
GenomeTraFac
LSPD: LIVER SPECIFIC GENE PROMOTER DATABASE (CSHL)
NEURAL NETWORK PROMOTER PREDICTION
NPRD: NUCLEOSOME POSITIONING REGION DATABASE
PlantPromDB
PLEIADES PROMOTER PROJECT
PromEC
PROMOSER
PROMOTER SCAN
PromoterSweep
PSCAN
S/MARt DB™
Vector Maps
CIRDNA
GENE INSPECTOR
IRESite
LINDNA
PlasMapper
PlasmID: PLASMID INFORMATION DATABASE
VECSCREEN (UNIVEC DATABASE)
VECTOR db
VECTOR MAPS (AGILENT)
VECTORDESIGNER™ (INVITROGEN)
VECTORS (PROMEGA)
VECTORS (RZPD)
Genomic Resources
Bioinformatics
Arena3D
ARGO GENOME BROWSER
AutoClass@IJM
BiNA: BIOLOGICAL NETWORK ANALYZER
BioCocoa
BIOCONDUCTOR
BioGRID: BIOLOGICAL GENERAL REPOSITORY FOR INTERACTION DATASETS
BioLayout EXPRESS 3D
BIOLOGICAL NETWORKS INTEGRATED RESEARCH ENVIRONMENT
BiOMART
BIOMOBY
BIOMODELS DATABASE (EMBL-EBI)
BIOMODELS.NET
BIOPATHWAYS CONSORTIUM
BioPAX: BIOLOGICAL PATHWAYS EXCHANGE
BIOPERL PROJECT
BIOPORTAL
BIOPYTHON PROJECT
BioTapestry
BioUML- OPEN SOURCE JAVA FRAMEWORK FOR SYSTEMS BIOLOGY
BMC BIOINFORMATICS
CALEYDO
CELLCIRCUITS
CELLDESIGNER™
CellML MODEL REPOSITORY
CellML TOOLs
COLLEXIS®
CVTree: COMPOSITION VECTOR PHYLOGENETIC ANALYSIS
CYTOSCAPE
DAS: DISTRIBUTED ANNOTATION SYSTEM
DAVID: DATABASE FOR ANNOTATION, VISUALIZATION AND INTEGRATED DISCOVERY
E-CELL
EBI: EUROPEAN BIOINFORMATICS INSTITUTE
EDINBURGH PATHWAY EDITOR
ENCODE: ENCYCLOPEDIA OF DNA ELEMENTS (NHGRI)
ENTREZ GENE (NCBI)
FGED: FUNCTIONAL GENOMICS DATA SOCIETY
GENDOO: GENE DISEASE FEATURES ONTOLOGY-BASED OVERVIEW
GeneAssist™ (APPLIED BIOSYSTEMS)
GENESPRING™
GENeVis
GenMAPP
GEO: GENE EXPRESSION OMNIBUS (NCBI)
GO: GENE ONTOLOGY CONSORTIUM
ImageWeb
INGENUITY PATHWAYS ANALYSIS
INOH: INTEGRATING NETWORK OBJECTS WITH HIERARCHIES
ISB: INSTITUTE FOR SYSTEMS BIOLOGY
J. CRAIG VENTER INSTITUTE SOFTWARE TOOLS
JWS ONLINE CELLULAR SYSTEMS MODELING
MGI GLOSSARY
MICROARRAY DATA ANALYSIS BIBLIOGRAPHY
MICROARRAY PROJECT (NHGRI)
MICROBIAL METAGENOMICS BIOINFORMATICS STRATEGY
MiGenAS: INTEGRATED GENE ANALYSIS SYSTEM
MIRIAM: MINIMAL INFORMATION REQUESTED IN THE ANNOTATION OF BIOCHEMICAL MODELS
myGRID
NAViGaTOR: NETWORK ANALYSIS VISUALIZATION AND GRAPHING TORONTO
Nbrowse
ODE: ONTOLOGICAL DISCOVERY ENVIRONMENT
OLS: ONTOLOGY LOOKUP SERVICE
OMNIGENE
ONDEX
OPENHELIX BIOINFORMATICS TRAINING
OSPREY
OWL: ONTOLOGY WEB LANGUAGE
PATTERN DISCOVERY GROUP (IBM)
PHOG: PHYLOFACTS ORTHOLOGY GROUP)
PosMed: POSITIONAL MEDLINE
PyNN: PYTHON NEURAL NETWORK MODELS
SAGEmap (NCBI)
SBGN: SYSTEMS BIOLOGY GRAPHIC NOTATION
SBML SOFTWARE MATRIX
SBML: SYSTEMS BIOLOGY MARKUP LANGUAGE
SENT: SEMANTIC FEATURES IN TEXT
SEQUENCE ANALYSIS WITH DISTRIBUTED RESOURCES (AN ONLINE COURSE)
SYSTEMS BIOLOGY WORKBENCH
TAVERNA
Tulip
VANTED: VISUALIZATION AND ANALYSIS OF NETWORKS CONTAINING EXPERIMENTAL DATA
visANT
WEBCELL
WhichGenes
yED
Clone Collections
CLONERANGER™
CLONES (ATCC)
DNASU PLASMID REPOSITORY
GENESERVICE
I.M.A.G.E. CONSORTIUM: iNTEGRATED MOLECULAR ANALYSIS OF GENOMES AND THEIR EXPRESSION
imaGenes
INVITROGEN CLONES
LINNEA™ GENES
MGC: MAMMALIAN GENE COLLECTION
OPEN BIOSYSTEMS
ORFEXPRESS™
ULTIMATE™ ORF BROWSER
Coparative Genomics
3D-GENOMICS
ARCHAEAL GENOME BROWSER (UCSC)
BBID: BIOLOGICAL BIOCHEMICAL IMAGE DATABASE
CHAOS+DIALIGN
CIRCOS
CMR: COMPREHENSIVE MICROBIAL RESOURCE (TIGR)
CORG: COMPARATIVE REGULATORY GENOMICS
CVTree: COMPOSITION VECTOR TREE
DATABASE OF ORTHOLOGOUS GROUPS
DEG:DATABASE OF ESSENTIAL GENES
e-PROTEIN
ECR BROWSER: EVOLUTIONARY CONSERVED REGIONS
eggNOG: EVOLUTIONARY GENEALOGY OF GENES--NON-SUPERVISED ORTHOLOGOUS GROUPS
EGO: EUKARYOTIC GENE ORTHOLOGUES
EPGD: EUKARYOTIC PARALOG GROUP DATABASE
ERGO™ (INTEGRATED GENOMICS)
eSHADOW: EVOLUTIONARY PHYLOGENETIC SHADOWING OF CLOSELY RELATED SPECIES (LLNL)
FOOTPRINTER MANUAL
FUSIONDB
GATA: GRAPHIC ALIGNMENT TOOL FOR COMPARATIVE SEQUENCE ANALYSIS
GENE INDEX PROJECT
GeneNest
GENETIC ANALYSIS SOFTWARE
GENOMES (EBI)
GENOMES FASTA
GESBAP: GENE SET BASED ANALYSIS OF POLYMORPHISMS
GIB: GENOME INFORMATION BROKER (DDBJ)
HGT-DB: HORIZONTAL GENE TRANSFER DATABASE
HOMOLOGENE
ICCARE: INTERSPECIFIC COMPARATIVE CLUSTERING AND ANNOTATION FOR EST
ICDS: INTERRUPTED CODING SEQUENCE DATABASE
IMG: INTEGRATED MICROBIAL GENOMES
InParanoid: EUKARYOTIC ORTHOLOG GROUPS
INTEGR8 (EMBL-EBI)
INTEROLOG/ REGULOG DATABASE
KALIGN
MaM: MULTIPLE ALIGNMENT MANIPULATOR
MANET: MOLECULAR ANCESTRY NETWORK
MBGD: MICROBIAL GENOME DATABASE
MEDEA (COMPARATIVE GENOMIC VISUALIZATION WITH ADOBE FLASH)
MEGA: MOLECULAR EVOLUTIONARY GENETICS ANALYSIS
MG-RAST: META GENOME RAPID ANNOTATION USING SUBSYSTEM TECHNOLOGY
MICROBIAL GENOME DATABASE FOR COMPARATIVE ANALYSIS
MICROFOOTPRINTER
MizBee: A MULTISCALE SYNTENY BROWSER
MrBayes
MULAN (LLNL)
NCBI TAXONOMY
ODB: OPERON DATABASE
OMICBROWSE (RIKEN)
OPTIC: ORTHOLOGOUS AND PARALOGOUS TRANSCRIPTS IN CLADES
ORTHOMCL DB
PANDIT: PROTEIN AND ASSOCIATED NUCLEOTIDE DOMAINS WITH INFERRED TREES
PANTHER: PROTEIN ANALYSIS THROUGH EVOLUTIONARY RELATIONSHIPS
PAUP: PHYLOGENETIC ANALYSIS USING PARSIMONY
PEDANT DATABASE
PHENOMICDB
PHOG: PHYLOFACTS ORTHOLOGY GROUP
PHYDBAC: PHYLOGENOMIC DISPLAY OF BACTERIAL GENES
PHYLIP
PHYLOMEDB
PHYLOPARS
PHYML
POPSET (NCBI)
POWER: PHYLOGENETIC WEB REPEATER
PROLINKS
SPLITSTREE: ANALYZING AND VISUALIZING EVOLUTIONARY DATA
SPRING: SORTING PERMUTATION BY REVERSALS AND BLOCK INTERCHANGES
SUPERFAMILY
SVC: STRUCTURED VISUALIZATION OF EVOLUTIONARY CONSERVED SEQUENCES
SYBIL (TIGR)
SynView
TAED: THE ADAPTIVE EVOLUTION DATABASE
TAXONOMY BROWSER (NCBI)
THE SEED
TREE OF LIFE
TREEBASE
TREEFAM
VISTA SERVERS
xBASE
Drosophila Genome
BDGP GOLD cDNA COLLECTION
BLAST Drosophila SEQUENCES
Drosophila GENOME RESOURCES (NCBI)
Drosophila MICROARRAY CENTRE
Drosophila POLYMORPHISM DATABASE
Drosophila RNAi SCREENING CENTER
FLIGHT
FLYBASE: A DATABASE OF Drosophila GENES AND GENOMES
FLYBRAIN
FLYMOVE
FlyTF: FLY TRANSCRIPTION FACTORS
FLYTRAP
FLYVIEW
GenomeRNAi
REDfly: REGULATORY ELEMENT DATABASE FOR DROSOPHILA
THE INTERACTIVE FLY
Fish Genomes
FISHSCOPE
MEDAKAFISH HOMEPAGE
ZEBRAFISH GENOME RESOURCES (NCBI)
ZFIN: ZEBRAFISH INFORMATION RESOURCE NETWORK
Fundamental Genomic Resources
ABySS-EXPLORER
ANNO-J
BAR CODE OF LIFE DATA SYSTEMS
BIOCONDUCTOR
BIOSAPIENS NETWORK
CBOL: CONSORTIUM FOR THE BARCODE OF LIFE
CLC GENOMICS MACHINE
DATABASE OF GENOME SIZES
DNASTAR®
e-ENSEMBL (EBI)
EBI TOOLBOX
ECR BROWSER: EVOLUTIONARY CONSERVED REGIONS
ENTREZ GENE
ENTREZ GENOME
GENETESTS
GENOME CHANNEL
GENOME GLOSSARY
GENOME REVIEWS (EBI)
GENOME WORKBENCH (NCBI)
GENOMES AT THE EBI
GenoViz
GOLD™ Genomes Online Database
HAWKEYE
IGV: INTEGRATIVE GENOMICS VIEWER
INSIGNIA
NCBI DCODE.ORG COMPARATIVE GENOMICS
NCBI SITE MAP
SAMtools
Fungal Genomes
BCCM: BELGIAN CO-ORDINATED COLLECTIONS OF MICRO-ORGANISMS
CADRE: CENTRAL Aspergillus DATA REPOSITORY
CANDIDADB
CGD: Candida GENOME DATABASE
ChromatinDB
DRYGIN:DATA REPOSITORY OF YEAST GENETIC INTERACTIONS
FUGOID: FUNCTIONAL GENOMICS OF ORGANELLAR INTRONS DATABASE
FUNGAL GENETICS STOCK CENTER
FUNGAL GENOMES BLAST
GENOLEVURES
MYCORWEB
Neurospora HOME PAGE
OGD: OOMYCETE GENOMICS DATABASE (NCGR)
ORIDB: REPLICATION ORIGINS DATABASE
PHI-BASE: PATHOGEN HOST INTERACTIONS
PHYTOPATHIC FUNGI DATABASE
PROPHECY: PROFILING PHENOTYPIC CHARACTERISTICS IN YEAST
Saccharomyces cerevisiae GENOME SNAPSHOT (SGD)
SCPD: PROMOTER DATABASE OF Saccharomyces cerevisiae (CSHL)
SGD: Saccharomyces GENOME DATABASE
snoRNAs FROM Saccharomyces
YEAST GENE ORDER BROWSER
YEAST INTRON DATABASE
YEAST RESOURCE CENTER
YEASTRACT: YEAST SEARCH FOR TRANSCRIPTIONAL REGULATORS AND CONSENSUS TRACKING
Gene Expression Databases
A-to-I RNA EDITING WEBSITE
ARRAYEXPRESS (EBI)
BASE: BioArray SOFTWARE ENVIRONMENT
BioGPS (SYMATLAS)
cDNA2Genome
ChimerDB
ChromatinDB
cMAP: CONNECTIVITY MAP
CORG: COMPARATIVE REGULATORY GENOMICS
COXPRESDB: CO-EXPRESSED GENE DATABASE
dbEST: EXPRESSED SEQUENCE TAGS DATABASE (NCBI)
dbGAP: DATABASE OF GENOTYPE AND PHENOTYPE (NCBI)
EUREXPRESS
EXPANDER: EXpression Analyzer and DisplayER)
fRNAdb
G-QUADRUPLEX RESOURCE SITE
GEMMA
GENECODIS: GENE ANNOTATIONS CO-OCURRENCE DISCOVERY
genepaint.org
GenMAPP
GEO: GENE EXPRESSION OMNIBUS
GREGLIST: POTENTIAL G-QUADRUPLEX -REGULATED GENES LIST
GSEA: GENE SET ENRICHMENT ANALYSIS
GXD: GENE EXPRESSION DATABASE
HHMD: HUMAN HISTONE MODIFICATION DATABASE
HuGE: HUMAN GENE EXPRESSION INDEX
HUGE: HUMAN UNIDENTIFIED GENE-ENCODED LARGE PROTEINS
IMPRINTED GENE CATALOG
IRESite
LIFEdb: DATABASE FOR LOCALIZATION, INTERACTION, FUNCTIONAL ASSAYS AND EXPRESSION OF PROTEINS
MGI: MOUSE GENOME INFORMATICS (GENE EXPRESSION LITERATURE QUERY)
MODEL MAKER (NCBI)
MSigDB: MOLECULAR SIGNATURES DATABASE
NATsDB: NATURAL ANTISENSE TRANSCRIPTS DATABASE
NCBI DCODE.ORG COMPARATIVE GENOMICS DEVELOPMENTS
ODE: ONTOLOGICAL DISCOVERY ENVIRONMENT
PhenoGen INFORMATICS
PolyA DB
POMELLO II
PROBEBASE
PRODORIC: PROKARYOTIC DATABASE OF GENE REGULATION
PSCAN
QuadBase: QUADRUPLEX DATABASES
RAD: RNA ABUNDANCE DATABASE
READ: RIKEN EXPRESSION ARRAY DATABASE
RECODE: A DATABASE OF TRANSLATIONAL RECODING EVENTS
REDI DB: RNA EDITING DATABASE
RELNET: RELEVANCE NETWORKS
RNAdb: NONCODING RNAs
SIDD: STRESS INDUCED DNA DUPLEX DESTABILIZATION
SMD: STANFORD MICROARRY DATABASE
SPLIGN (NCBI)
SwissRegulon
ToppGene SUITE
UNIGENE
UTRdb
VisHiC: VISUALIZATION OF HIERARCHICAL CLUSTERING
WebGMAP
Gene Symbols and Annotation
ARGH: BIOMEDICAL ACRONYM RESOLVER
BABELOMICS
BARCODE OF LIFE
BASys: BACTERIAL ANNOTATION SYSTEM
BioGPS
BOLD: BAR CODE OF LIFE DATA SYSTEMS
cDNA2Genome
COFECO: COMPOSITE FUNCTION ANNOTATION ENRICHED BY PROTEIN COMPLEX DATA
DAVID: DATABASE FOR ANNOTATION, VISUALIZATION AND INTEGRATED DISCOVERY
e!ENSEMBL
ECfunction: FUNCTIONAL ANNOTATION VIEWER
ENTREZ GENE (NCBI)
GenDB
GENECODIS: GENE ANNOTATIONS CO-OCURRENCE DISCOVERY
GO PaD: GENE ONTOLOGY PARTITION DATABASE
GO: GENE ONTOLOGY
GOA: GENE ONTOLOGY ANNOTATION (EMBL-EBI)
GOblet
GoGene
GOPET
GPSDB: GENE AND PROTEIN SYNONYM DATABASE
GUIDELINES FOR HUMAN GENE NOMENCLATURE
HARVARD GENE FUNCTIONAL ANNOTATION PREDICTION BROWSER
HGNC: HUGO GENE NOMENCLATURE COMMITTEE
HGNC: HUMAN GENE NOMENCLATURE SEARCH
IPNI: INTERNATIONAL PLANT NAMES INDEX
IUBMB NOMENCLATURE
IUPAC NOMENCLATURE
KLAM: KIM LAB ANNOTATION MAPPER
MICHECK:MICROBIAL GENOME CHECKER
MOLECULE PAGES (AfCS)
MOUSE NOMENCLATURE
PICR: PROTEIN IDENTIFIER CROSS-REFERENCE SERVICE
PLANT ONTOLOGY DATABASE
PROTEIN NAMING UTILITY
REFSEQ (NCBI)
TOPPGENE SUITE
TROPICOS
UMLSKS: UMLS KNOWLEDGE SOURCE SERVER
VLAD: VisuaL Annotation Display
WEGO: WEB GENE ONTOLOGY