GenomicDB

MGI: http://www.informatics.jax.org/

Ensembl: http://www.ensembl.org/

Gene Cards: http://www.genecards.org/

GenomeNet: http://www.genome.ad.jp/

HUGO: http://www.gene.ucl.ac.uk/nomenclature/

NCBI: http://www.ncbi.nlm.nih.gov/

SCIRUS: http://www.scirus.com/srsapp/

UCSC Genome Bioinformatics: http://genome.ucsc.edu/

Microarray

DNA Microarray (Genome Chip): http://www.gene-chips.com/

Expression Profiler (Jaak Vilo, EBI): http://ep.ebi.ac.uk/EP/

Microarray Gene Expression Data Society - MGED Society: http://www.mged.org/

READ Riken Expression Array Database: http://read.gsc.riken.go.jp/

RMAExpress: http://www.stat.berkeley.edu/~bolstad/RMAExpress/RMAExpress.html

Scanalytics MicroArray Suite: http://www.scanalytics.com/index.shtml

SAM: Significance Analysis of Microarrays: http://www-stat.stanford.edu/~tibs/SAM/

GeneSpring Support & Training: http://www.chem.agilent.com/Scripts/Generic.ASP?lPage=35084&indcol=Y&prodcol=Y

Silicon Genetics Webinar Course Listing: http://www.silicongenetics.com/cgi/SiG.cgi/Support/webinars.smf

Spotfire, Inc. Webcasts: http://www.spotfire.com/?CFID=565126&CFTOKEN=76884436

DRAGON Database: http://pevsnerlab.kennedykrieger.org/dragon.htm

Limma: http://bioinf.wehi.edu.au/limmaGUI/

Limma – affylmGUI: http://bioinf.wehi.edu.au/affylmGUI/

Genomics Institute of the Novartis Research Foundation (GNF): http://symatlas.gnf.org/SymAtlas/

Bioinformatics Institution and Tools

Bioinformatics Sequence and Genome Analysis: http://www.bioinformaticsonline.org/

Geo.Church, CCG: http://arep.med.harvard.edu/

Globin Gene Server: http://globin.cse.psu.edu/

The Institute for Genomic Research – Software Tools: http://www.tigr.org/software/

EBI Tools Sequence Analysis, Sequence Translation, Validation, Alignments, Gene Prediction: www.ebi.ac.uk/Tools/sequence.html

Prediction: http://www.ebi.ac.uk/Tools/sequence.html

Bioinformatics Link: http://bioinformatics.ca/bioinformatics_resources/links/

Bioinformatics Link (UCSC): http://genome.ucsc.edu/bestlinks.html

Annotation

Gene Ontology: http://www.geneontology.org/

Gene Ontology Software and Databases: http://www.godatabase.org/dev/

GoFish: http://llama.med.harvard.edu/~berriz/GoFishWelcome.html

Pub Gene: http://www.pubgene.org/

Source Search: genome-www5.stanford.edu/cgi-bin/source/sourceSearch

FatiGO: http://www.fatigo.org/

David GO: http://david.niaid.nih.gov/david/ease.htm

Onto-Express: http://vortex.cs.wayne.edu/Projects.html

Boulder Data Interchange Format: http://stein.cshl.org/software/boulder/

Gene Prediction

BDGP Genie Gene Finder Based on Generalized Hidden Markov Models: www.fruitfly.org/seq_tools/genie.html

Eukaryotic GeneMark.hmm: http://opal.biology.gatech.edu/GeneMark/eukhmm.cgi#prot

Gene Finding Programs: http://cmgm.stanford.edu/classes/genefind/

GeneMark: http://www.ebi.ac.uk/genemark/

GeneMark ™ -Gene prediction software program: http://opal.biology.gatech.edu/GeneMark/

GeneSeqer: http://www.bioinformatics.iastate.edu/cgi-bin/gs.cgi

New GENSCAN Web Server at MIT: http://genes.mit.edu/GENSCAN.html

GLIMMER: http://www.tigr.org/software/glimmer/

Pathway

Biochemistry Online: http://employees.csbsju.edu/hjakubowski/default.html

GenMAPP: http://www.genmapp.org/introduction.asp

FatiWise.cgi: http://fatiwise.bioinfo.ochoa.fib.es/cgi-bin/FatiWise.cgi

Training IobionLab PathwayAssist: www.iobion.com/support/support_PA_manualpage.html

Promoter Analysis

AlignACE: http://atlas.med.harvard.edu/

EPD Sequence Download page: www.epd.isb-sib.ch/seq_download.html

Gene Regulation: http://www.gene-regulation.com/

Genomatix: http://www.genomatix.de/index.html

Motif Sampler: http://www.esat.kuleuven.ac.be/~thijs/Work/MotifSampler.html

RSA-tools: http://rsat.ulb.ac.be/rsat/

TFSFARCH: http://150.82.196.184/research/db/TFSEARCH.html

Zhang Rotation, Promoter Analysis of Co-regulated Transcripts in Mouse Cells: http://cgsigma.cshl.org/thomase/

Upstream sequences for human and mouse Refseq mRNAs: http://arep.med.harvard.edu/labgc/adnan/hsmmupstream/

Protein Analysis

DIP - Database of Interacting Proteins: http://dip.doe-mbi.ucla.edu/dip/

DIPBrowse: http://dip.doe-mbi.ucla.edu/dip/

ExPASy Proteomics Server: http://ca.expasy.org/

CombSearch Help: http://us.expasy.org/tools/CombSearch/cbhelp.html

InterProScan Sequence Search: http://www.ebi.ac.uk/InterProScan/

iProClass: http://pir.georgetown.edu/iproclass/

Pfam: Protein Search: http://pfam.wustl.edu/hmmsearch.shtml

Sequence Analysis

Advanced PipMaker: http://pipmaker.bx.psu.edu/cgi-bin/pipmaker?advanced

Pôle Bioinformatique Lyonnais: http://pbil.univ-lyon1.fr/

Sequence formats conversions: http://bioweb.pasteur.fr/seqanal/formats-uk.html

The USC Sequence Alignment Server: http://hto-13.usc.edu/software/seqaln/seqaln-query.html

GeneHuggers - tools for biological discovery in sequenced genomes: http://www.scripps.edu/rc/softwaredocs/gh/

Sanger: http://www.sanger.ac.uk/

CCHMC Internal

Pulmonary Biology Gene Expression: http://pbge.cchmc.org

Anil's http://anil.cchmc.org

Jarek's http://folding.cchmc.org

GeneServer: http://genome.chmcc.org/geneserver/

Signet: http://cypher.cchmc.org:1104/servlet/GeNet

CisMols: http://cismols.cchmc.org/peak-web/index.jsp

University of Cincinnati GML Homepage: http://microarray.uc.edu/

GenomeTraFac: http://genometrafac.cchmc.org/genome-trafac/index.jsp

UC Libraries: http://www.libraries.uc.edu/

Download Scripts

Cluster Bluster Parse

Confidence Score