| ENSEMBL | Complete genome viewer for a variety of organisms including human, fugu, dog etc |
| AtENSEMBL | Arabidopsis Ensembl viewer |
| EMBL | European Bioinformatics Institue database of DNA and protein sequences for all organisms |
| NCBI | Database of DNA and protein sequences for all organisms |
| BLAST | Search databases using DNA or protein sequences to identify homologous sequences |
| FASTA | Search databases using DNA or protein sequences to identify homologous sequences |
| ClustalW | Align multiple DNA or protein sequences |
| GeneMark | Identifies coding regions within a DNA sequence |
| Transeq | Translate DNA sequences into protein sequences |
| Restriction analysis | Identify restriction enzyme sites within a DNA sequence |
| Reverse complement | Produce the reverse complement of a DNA sequence or change single stranded into double stranded sequence |
| TRES | Transcription regulatory element search. Search promoter sequences for known regulatory motifs |
| PlantCARE | Search plant promoters for known regulatory motifs |
| OTFBS | Over-represented transcription factor binding site prediction tool. Detects over-represented motifs in a set of promoter sequences |
| NASCarrays | Arabidopsis Affymetrix database |
| ArrayExpress | Database of Affy and micro arrays for all organisms at EBI |
| EPCLUST | Tool for clutser analysis of array data |
| Spot History | Displays a genes pattern of expression over all the slides in the Arabidopsis NASCarray database |
| Two gene scatter plot | Compares 2 genes expression levels as a scatter plot over all the slides in the Arabidopsis NASCarray database |
| Gene swinger | Shows in which experiments a gene of interest changed the most |
| Genevestigator | Analysis tools for Arabidopsis affy data |
| SMART | Simple Modular Architecture Research Tool. Analyse protein sequences for known domains |
| PROSITE | Database of protein families and domains |
| Pfam | Analyse protein sequence for functional domains |
| CPHmodels | Predicts protein structure |
| COILS | Predicts coiled regions in a protein sequence |
| TMpred | Predicts transmembrane domains |
| SignalP | Predicts signal peptide cleavage sites |
| KEGG | Kyoto Encyclopedia of Genes and Genomes. Includes database of pathways including metabolic, regulatory, disease, circadium etc. |
| AraCyc | Arabidopsis biochemical pathways. Can overlay transcriptomics, proteomics data. |