1) Database Search
| Genome Net (The University of Tokyo and Kyoto University) | GenBank, EMBL,etc. |
| EMBL (EBI) | Nucleic acid database |
| Genbank (NCBI) | Nucleic acid database |
| Entrez／NCBI（NIH) | Search for references and sequences |
| GDB(JST) | Database of genome map (mirror site) |
| Genome Channel (ORNL) | Comprehensive sequence-based view of genomes |
| Ribosomal Database Project II (MSU) | Ribosomal Database Project (RDP) |
| The Sanger Center | |
| SRS（National Institute of Genetics） | Keyword search on DDBJ |
| TESS (CBH) | Transcription Element Search System |
| TIGR (The Institute for Genomic Research) | A collection of genomic databases for microbes, plants, and animals |
| Mouse (NCBI) | |
| VirGO | Viral Genome Database |
| Animal Genome Research Program (National Institute of Agrobiological Sciences and Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries) | |
| E.Coli Genome Project (University of Wisconsin - Madison) | |
| Genome Information Broker（National Institute of Genetics） | Browser of complete microbial genomes |
| HIV Sequence Database | |
| KDRI Database (Kazusa DNA Research Institute) | CyanoBase, Arabidopsis thaliana, Human cDNA, etc. |
| MIPS (Munich Information Center for Protein Sequences) | Yeast, Arabidopsis thaliana, Neurospora crassa, etc. |
| Pseudomonas Genome Project | Pseudomonas aeruginosa |
| RATMAP (Goteborg University) | The Rat Genome Database |
| SGDTM (Stanford Univ.) | Saccharomyces cerevisiae |
| Human-Mouse Homology Map (NCBI) |
| Genome Net (The University of Tokyo and Kyoto University) | Blast, Fasta |
| DDBJ（National Institute of Genetics） | Blast, PSI-blast, fasta, Smith-Waterman |
| NIAS DNAbank SWsrch Service (DNAbank, the Ministry of Agriculture, Forestry and Fisheries) | Smith-Waterman |
| EBI | Smith-Waterman |
| Gene Quest (ORNL) | Blast, Fasta, Smith-Waterman etc. |
| NCBI (NIH) | Blast |
| Gene Finder (Frontiers in Bioscience) | Splice site prediction, coding region prediction, etc. |
| GeneMark (Georgia Inst. of Tech.) | Hidden Marcov model |
| GENSCAN (MIT) | Hidden Marcov model |
| GeneBuilder (ITBA) | An integrated computing system for protein-coding gene prediction |
| HCpolya (ITBA) | Hamming Clustering poly-A prediction in Eukaryotic Genes |
| HCtata (ITBA) | Hamming-Clustering Method for TATA Signal Prediction in Eukaryotic Genes |
| GenView (ITBA) | Protein-Coding Gene Prediction |
| Genie (UCSC) [Human] | Hidden Marcov model |
| HMMGene (Tech. Univ. Denmaark) | Prediction of vertebrate and C. elegans genes with HMM |
| PROCRUSTES (USC) | Gene Recognition via Spliced Alignment |
| GRAIL (ORNL) | Neural network, etc. |
| GrailEXP (ORNL) | Improved version of Grail |
| Generation (ORNL) | Microbial Gene Prediction System |
| FramePlot (National Institute of Infectious Diseases) | Frame analysis of high GC content bacteria |
| ORF Seeker (embl-heiderberg) | ORF search and translation |
| NCBI | ORF Finder |
| Web Cutter 2 | Restriction map |
| GeneFisher (Bielefeld Univ.) | |
| Primer3 (MIT) | |
| Web Primer (SGDTM, Stanford Univ.) | |
| CODEHOP (FHCRC) | COnsensus-DEgenerate Hybrid Oligonucleotide Primers |
| DDBJ (National Institute of Genetics) | SAKURA |
| Genbank (NCBI) | BankIt |
| Promoter Predictor (Berkley Drosophia Genome Project) | Prediction of promoter region |
| Proscan (BIMAS) | Prediction of promoter region |
| Promotor 2.0 (CBS) | Prediction of promoter region |
| Splice Site Prediction (Berkley Drosophia Genome Project) | Prediction of splice sites |
| NetGene2 (CBS) | Prediction of splice sites (human, C.elegance, A.thaliana) |
| NetPlantGene (CBS) | Prediction of splice sites (Arabidopsis Thaliana) |
| SpliceView (ITBA) | Splice Prediction by using Consensus Sequences |
| UniSTS (NCBI) | Electronic PCR |