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