1. Databases
1.1. Sequences
1.2. RNA
1.3. Comparative & Phylogenetic
- COG: Phylogeneticclassification of proteins
- TreeBase: Adatabase of phylogenetic knowledge
- XREF: Cross-referencing with model organisms
- HomoloGene: Genehomologies across species
1.4. SNPs, Mutations & Variations
- dbSNP: Singlenucleotide polymorphism database at NCBI
- HapMap: International HapMap Project
- HGVbase : HumanGenome Variation Database
1.5. Microarray & Gene Regulation
- GEO: Geneexpression omnibus NCBI
- Array Express
- SMD: StanfordMicroArray Database
- ChipDB
- TRRD: Transcription Regulatory region database
- TRANSFAC
- JASPA
- The Signaling Gateway
1.6. Proteins & Interactions
- InterPro
- ExPASy Proteomics: Expert ProteinAnalysis System
- PRIDE
- OPD : OpenProteomics Database
- BioGrid
- BIND
- HPRD
- DIP
- MiMI
- NetPhos 2.0 Server
- NetOGlyc 3.1 Server
1.7. Reaction Pathways
1.8. Enzyme Databases
1.9. Membrane Transporters
1.10. Glycosylation
1.11. Protein Structure
1.12. Systems Biology
1.13. Synthetic Biology
2. Computational Tools
2.1. Genome Browser
2.2. Sequences Comparison & Alignment
- NCBI BLAST
- WU-BLAST
- ClustalW: Multiple sequence alignment
- CINEMA: Colour interactive editor formultiple alignments
- FASTA
2.3. Promotor & Transcription Regulation
- Promotor Scan: Promoter regions based on scoring homologies with putative eukaryoticPol II promoter sequences
- MatInspector: Detection of transciption factor binding sites
- TESS: Transcription Element Search System
- E. coli DNA-Binding Site
2.4. Microarray & Gene Regulation
- MIAME Minimum information about amicroarray experiment
- MeV: MultiExperiment Viewer
- GenePattern
- geWorkBench
- Bioconductor
- Agilent eArray
- DAVID
2.5. Membrane Protein Analysis
2.6. Proteomics / Mass Spectrometry
2.7. Protein Structure Visualization
2.8. Metabolism
2.9. Pathways
2.10. RNA folding
2.11. Oligomer Microarray Design
2.12. Protein 2-D Structure
2.13. Protein 3-D Structure
2.14. Systems Biology
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