1. Databases

1.1. Sequences

1.1.1. DDBJ : http://www.ddbj.nig.ac.jp/

1.1.2. EMBL : http://www.embl.org/

1.1.3. GenBank : http://www.ncbi.nlm.nih.gov/Genbank/

1.1.4. GenBank ftp site: ftp://ftp.ncbi.nih.gov/genbank/genomes/

1.1.5. TIGR: http://www.tigr.org/

1.1.6. Wellcome Trust Sanger Institute: http://www.sanger.ac.uk/

1.2. RNA

1.2.1. Rfam: RNA familiy database http://www.sanger.ac.uk/Software/Rfam/

1.2.2. RNA base: Databaseof RNA structures http://mbcr.bcm.tmc.edu/smallRNA/smallrna.html

1.2.3. sRNA: Small RNAdatabase http://mbcr.bcm.tmc.edu/smallRNA/smallrna.html

1.3. Comparative & Phylogenetic

1.3.1. COG: Phylogeneticclassification of proteins http://www.ncbi.nlm.nih.gov/COG/

1.3.2. TreeBase: Adatabase of phylogenetic knowledge http://treebase.bio.buffalo.edu/treebase/

1.3.3. XREF: Cross-referencing with model organisms http://www.ncbi.nlm.nih.gov/XREFdb/

1.3.4. HomoloGene: Genehomologies across species http://www.ncbi.nlm.nih.gov/HomoloGene/

1.4. SNPs, Mutations & Variations

1.4.1. dbSNP: Singlenucleotide polymorphism database at NCBI http://www.ncbi.nlm.nih.gov/projects/SNP/

1.4.2. HapMap: International HapMap Project http://www.hapmap.org/

1.4.3. HGVbase : HumanGenome Variation Database http://www.hgvbase.org/

1.5. Microarray & Gene Regulation

1.5.1. GEO: Geneexpression omnibus NCBI http://www.ncbi.nlm.nih.gov/geo/

1.5.2. Array Express: http://www.ebi.ac.uk/microarray/

1.5.3. SMD: StanfordMicroArray Database http://genome-www5.stanford.edu/

1.5.4. ChipDB: http://staffa.wi.mit.edu/chipdb/public/

1.5.5. TRRD: Transcription Regulatory region database http://wwwmgs.bionet.nsc.ru/mgs/gnw/trrd/

1.5.6. TRANSFAC: http://www.gene-regulation.com/pub/databases

1.5.7. JASPA: http://jaspar.genereg.net/

1.5.8. The Signaling Gateway: http://www.signaling-gateway.org/

1.6. Proteins & Interactions

1.6.1. InterPro : http://www.ebi.ac.uk/interpro/

1.6.2. ExPASy Proteomics: Expert ProteinAnalysis System http://ca.expasy.org/

1.6.3. PRIDE: http://www.ebi.ac.uk/pride/

1.6.4. OPD : OpenProteomics Database http://bioinformatics.icmb.utexas.edu/OPD/

1.6.5. BioGrid: http://www.thebiogrid.org/

1.6.6. BIND: http://www.bind.ca/

1.6.7. HPRD: http://www.hprd.org/

1.6.8. DIP: http://dip.doe-mbi.ucla.edu/

1.6.9. MiMI: http://mimi.ncibi.org/MiMI/home.jsp

1.7. Reaction Pathways

1.7.1. KEGG: Kyoto Encyclopedia of Genes and Genomes http://www.genome.jp/kegg/

1.7.2. KEGG ftp site: ftp://ftp.genome.jp/../pub/kegg/

1.7.3. Biocarta: http://www.biocarta.com/

1.7.4. BioCyc: http://www.biocyc.org/

1.8. Enzyme Databases

1.8.1. BRENDA: http://www.brenda-enzymes.info/

1.9. Membrane Transporters

1.9.1. TransportClassification Database: http://www.tcdb.org/

1.9.2. TransportDB: http://www.membranetransport.org/

1.10. Glycosylation

1.10.1. Functional Glycomics: http://www.functionalglycomics.org/static/

1.10.2. Bacterial Carbohydrate Structural Database: http://www.glyco.ac.ru/bcsdb/start.shtml

1.11. Protein Structure

1.11.1. Protein Data Bank: http://www.rcsb.org/pdb/home/home.do

1.11.2. CATH: http://www.cathdb.info/latest/index.html

1.11.3. Protein Information Resource: http://www-nbrf.georgetown.edu/cgi-bin

1.11.4. Structural Classification of Proteins: http://scop.mrc-lmb.cam.ac.uk/scop/index.html

1.11.5. Swiss-Prot: http://www.ebi.ac.uk/swissprot/

1.12. Systems Biology

1.12.1. BiGG Database: http://bigg.ucsd.edu/

1.13. Synthetic Biology

1.13.1. Standard Biological Parts: http://parts.mit.edu/registry/index.php/

1.14. Other

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

1.14.2. PubMed: http://www.ncbi.nlm.nih.gov/sites/pubmed

2. Computational Tools

2.1. Genome Browser

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

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

2.1.3. UCSC : http://genome.ucsc.edu/

2.2. Sequences Comparison & Alignment:

2.2.1. NCBI BLAST: http://www.ncbi.nlm.nih.gov/blast/Blast.cgi

2.2.2. WU-BLAST: http://blast.wustl.edu/

2.2.3. ClustalW: Multiple sequence alignment http://www.ebi.ac.uk/Tools/clustalw2/

2.2.4. CINEMA: Colour interactive editor formultiple alignments http://www.bioinf.manchester.ac.uk/dbbrowser

2.2.5. FASTA: http://www.ebi.ac.uk/fasta33/

2.3. Promotor & Transcription Regulation

2.3.1. Promotor Scan: Promoter regions based on scoring homologies with putative eukaryoticPol II promoter sequences http://www-bimas.cit.nih.gov/molbio/proscan/

2.3.2. MatInspector: Detection of transciption factor binding sites http://www.genomatix.de/products/MatInspector/

2.3.3. TESS: Transcription Element Search System http://www.cbil.upenn.edu/cgi-bin/tess/tess

2.3.4. E. coli DNA-Binding Site: http://arep.med.harvard.edu/ecoli_matrices/

2.4. Microarray & Gene Regulation

2.4.1. MIAME Minimum information about amicroarray experiment http://www.mged.org/Workgroups/MIAME/miame

2.4.2. MeV: MultiExperiment Viewer http://www.tm4.org/mev.html

2.4.3. GenePattern: http://www.broad.mit.edu/cancer/software/

2.4.4. geWorkBench: http://magnet.c2b2.columbia.edu/geworkbench

2.4.5. Bioconductor: https://cabig.nci.nih.gov/tools/Bioconductor

2.4.6. Agilent eArray: https://earray.chem.agilent.com/earray/

2.4.7. DAVID: http://david.abcc.ncifcrf.gov/home.jsp

2.5. Membrane Protein Analysis

2.5.1. DAS: Transmembrane sequence prediction http://www.sbc.su.se/%7Emiklos/DAS/

2.6. Proteomics / Mass Spectrometry

2.6.1. ExPASy Tools: http://ca.expasy.org/tools/

2.7. Protein Structure Visualization

2.7.1. PYMOL: http://pymol.sourceforge.net/

2.8. Metabolism

2.8.1. CellNetAnalyzer / FluxAnalyzer: http://www.mpi-magdeburg.mpg.de/projects/cna

2.8.2. COBRA Toolbox: http://gcrg.ucsd.edu/Downloads/Cobra_Toolbox

2.8.3. FBA: http://gcrg.ucsd.edu/Downloads/Flux_Balance

2.9. Pathway

2.9.1. GenMapp: http://www.genmapp.org/

2.9.2. KEGG Tools: http://www.genome.jp/kegg/kegg2.html

2.9.3. GSEA: Gene SetEnrichment Analysis http://www.broad.mit.edu/gsea/

2.9.4. Extreme Pathway Analysis: http://gcrg.ucsd.edu/Downloads/Extreme

2.9.5. PUMA2: http://compbio.mcs.anl.gov/puma2/cgi-bin

2.10. RNA folding

2.10.1. Mfold: http://frontend.bioinfo.rpi.edu/rna-form1.cgi

2.10.2. Sfold: http://sfold.wadsworth.org/index.pl

2.10.3. siRNA SelectionProgram: http://jura.wi.mit.edu/bioc/siRNAext/home.php

2.10.4. Vienna: http://www.tbi.univie.ac.at/~ivo/RNA/

2.11. Oligomer Microarray Design

2.11.1. ArrayOligoSelector: http://arrayoligosel.sourceforge.net/

2.11.2. OligoArray 2.0: http://berry.engin.umich.edu/oligoarray2/

2.11.3. OligoPicker: http://pga.mgh.harvard.edu/oligopicker/

2.11.4. OligoWiz 2.0 http://www.cbs.dtu.dk/services/OligoWiz2/

2.11.5. Picky: http://www.complex.iastate.edu/download/Picky/

2.11.6. ROSO: http://pbil.univ-lyon1.fr/roso/Home.php

2.11.7. YODA: http://pathport.vbi.vt.edu/YODA/

2.11.8. GoArrays: http://www.isima.fr/bioinfo/goarrays/

2.11.9. OligoSpawn: http://138.23.191.145/

2.11.10. EC Oligos: ftp://ftp.ebi.ac.uk/pub/software/dos/EC_oligos/

2.12. Protein 2-D Structure

2.12.1. Chou-Fasman: http://fasta.bioch.virginia.edu/

2.12.2. NNpredict: http://alexander.compbio.ucsf.edu/~nomi

2.12.3. PredictProtein: http://www.predictprotein.org/

2.12.4. SCRATCH: http://www.igb.uci.edu/?page=tools&subPage

2.13. Protein 3-D Structure

2.13.1. 3D-PSSM: http://www.sbg.bio.ic.ac.uk/~3dpssm/

2.13.2. CPHmodels 2.0: http://www.cbs.dtu.dk/services/CPHmodels/

2.13.3. UCLA-DOE: http://fold.doe-mbi.ucla.edu/

2.13.4. Topology of Protein Structure: http://www.tops.leeds.ac.uk/

2.14. Systems Biology

2.14.1. Cytoscape: http://www.cytoscape.org/

2.14.2. Systems Biology Workbench: http://www.sys-bio.org/research/sbwIntro.htm

2.14.3. Ingenuity: www.ingenuity.com

2.14.4. GeneGo: http://www.genego.com/

2.14.5. Gene Designer: http://www.dna20.com/commerce/customer/

2.14.6. Systems Biology Markup Language: http://sbml.org/index.psp

2.14.7. Bioinformatics.net: http://www.bioinformatics.vg/index4.shtml

2.14.8. Biowww.net: http://biowww.net/

2.14.9. Tools at Weiznmann Institute: http://bip.weizmann.ac.il/