| 1.Genome data | Type | Website Name | Description, Help info | example screens |
| NIGMS | agency | Nat. Inst. of General Medical Sciences: Structural Genomics | Protein Structure Initiative | |
| Ensembl | annotation | EBI/Sanger Automatic Annotation db | Documentation and Getting Started with Ensembl | |
| TIGR BACs | BAC ends | TIGR BAC-end sequences | Search TIGR BAC ends database | |
| Apollo | browser | Apollo Drosophila/generic genome viewer & editor | Apollo user guide | |
| HGREP | browser | RIKEN Genome Sciences Human Genome REconstruction Project | | |
| UCSC Genome Browser | browser | UCSC Working Draft Genome Browser | search UCSC working draft genome sequence by position | |
| UCSD Genome Browser | browser | UCSD Genome Browser | Human Genome Browser User Guide | |
| UCSD Table Browser | browser | UCSD Table Browser | UCSC Table Browser Help | |
| JGI | DNA | DOE Joint Genome Institute | DOE production sequencing site, numerous species | |
| UCSC | DNA | UCSC Assembled Draft DNA Sequence | all publically available genome sequence, assembled | algorithms |
| dbEST | ESTs | NCBI Expressed Sequence Tag database | NCBI Expressed-sequence Tag (EST) search page | |
| Gene Indices | ESTs | TIGR Gene Indices | analysis of transcribed sequences in public EST data | |
| STACK | ESTs | S. Africa National Bioinformatics Inst. | StackPack WebBlast guide | |
| GDB | genes | The Genome Data Base (int'l collaboration) | repository for Human Genome Initiative mapping data | |
| OMIM | genes | Online Mendelian Inheritance in Man (NCBI) | OMIM home and search page, with links to related sites | |
| UniGene | genes | NCBI Non-redundant sequence db:Unigene | NCBI Non-redundant (Unigene) resource page | |
| BCM search-launcher | Homol srch | Baylor (homology) Search-launcher | collection of homology and other tools | |
| BLAST | Homol srch | NCBI's Basic Local Alignment/Search Tool | multiple variants of the BLAST homology search tool | |
| Blast2 at Genestream | Homol srch | Blast2 at Genestream (France) | BLAST Search main parameters | |
| BLAT | Homol srch | UCSC Working Draft search tool | homology search (not BLAST) of UCSC working draft | |
| FASTA | Homol srch | FASTA Programs at the U. of Virginia | | |
| NA search-launcher | Homol srch | BCM Search Launcher: Nucleic Acid Sequence Searches | nucleic acid homology search tools | |
| DDBJ | multiple dbs | DNA Databank of Japan | | |
| EMBL | multiple dbs | EMBL-EBI Nucleotide Sequence DB | EMBL Documentation | |
| ExPaSy | multiple dbs | Swiss Inst. Of Bioinformatics Mol. Bio. Server | multiple dbs, dna and proteomics tools and links | |
| Kegg | multiple dbs | Kyoto Encyclopedia of Genes and Genomes | | |
| NCBI Blastable DBs | multiple dbs | NCBI Blastable DBs | list of NCBI databases available for BLAST homology searches | |
| NHGRI Genome Hub | multiple dbs | NHGRI Genome Hub | | |
| Whitehead | multiple dbs | Whitehead Institute/MIT Genome Research Ctr | genome maps, databases & tools, incl mouse & rat | |
| GenomeWeb | multiple dbs | HGMP Genome Database list | | |
| ALFRED | Mutations | Yale Allele Frequency Database | About ALFRED | |
| Protein Mutant Database | Mutations | Protein Mutant Database | How to Use DBGET/LinkDB | |
| Universal Mutation Database | Mutations | Software and databases for mutations in human genes | | |
| PDB | Protein | Protein Data Bank | Protein Data Bank: search by ID or field match | |
| Prosite | Protein | Prosite DB of Proteins Families and Domains | Protein family and domain keyword search site | |
| SCOP | Protein | Structural Classification of Protein (SCOP) mirrors | links to servers of the Structural Classification of Proteins DB | |
| Swiss-Prot | Protein | SwissProt Protein Database | searchable annotated protein sequence database | |
| VAST | Protein | Vector Alignment Search Tool | tool for retrieving related 3D structures from MMDB | |
| CSH sppgb | SNPs | SNP Consortium | home page and search tool | |
| dbSNP | SNPs | NCBI dbSNP | NCBI SNP search page | |
| Human SNP Database | SNPs | Whitehead Inst. Human SNP Database | The SNP FAQ page | |
| Genestream ALIGN server | tools | Genestream Align server | Align search help | |
| Genestream LALIGN server | tools | Genestream Lalign Server | lalign Search Help | |
| RepeatMasker | tools | WU RepeatMasker Web Server | RepeatMasker documentation | |
| 2. Annotation | Type | Website Name | Description, Help info | |
| Artemis | browser/editor | Sanger DNA sequence viewer and annotation tool | Artemis user manual | |
| Pipmaker | comparative | PIPmaker Percent Identity Plot tool | PipMaker Instructions | PipMaker Examples |
| VISTA | comparative | LBNL VISualization Tool for Alignments | VisTA overview | Example Vista |
| Annot: Haussler | DNA | UCSC Genome Browser Database | Human Genome Browser | |
| Banbury Cross | gene predictio | Gene Identification Software Benchmarking" | | |
| GeneFinder | gene prediction | Phil Green's Genefinder server | | |
| Geneid | gene prediction | Genome Informatics Research Lab, Geneid | | |
| Genie | gene prediction | UCSC/LBNL Gene Prediction tool | Genie Limitations | Genie Example |
| Genscan | gene prediction | MIT Genscan server | GENSCAN Information | |
| GRAIL | gene prediction | ORNL Gene Recognition & Ass'y Internet Link | Manual for GRAIL & Grailexp | |
| Grailexp | gene prediction | Grail Experimental Gene Discovery Suite | Grailexp FAQ | |
| HMMGene | gene prediction | Denmark Ctr for Biological Seq. Analaysis | HMMGene Documentation | |
| MZEF | gene prediction | CSHL - Michael Zhang Exon Finder tool | MZEF Readme | |
| Procrustes | gene prediction | USC -> UCSD Procrustes WWW server | Procrustes system | Procrustes prediction example |
| ISIS | Introns | Intron Sequence and Information database | Intron Sequence and Information database | Example Analysis of Alternate Splicing in Human Genes |
| Celera Discovery for Academia | multiple dbs | Celera Discovery System | | |
| TIGR | multiple dbs | The Institute for Genomic Research databases | TIGR FAQ | |
| FIDD | Mutations | Frequency of Inherited Disorders Database | FIDD Background | |
| GenomeWeb | Mutations | Human Mutation Databases (List of websites) | Detailed information on Mutation DBs | |
| HGMD | Mutations | Human Gene Mutation Database | HGMD Background | |
| Tbase | Mutations | The Transgenic/Targeted Mutation Database | Instructions for Searching TBASE | |
| AACompIdent | Protein | identify protein from its amino acid composition | AACompIdent documenatation | |
| AACompSim | Protein | compare amino acid compositions | AACompSim documentation | |
| CATH | Protein | Protein Structure Classification | CATH Detailed information | |
| CE | Protein | Combinatorial Extension of the optimal path | Combinatorial Extension (CE) - Help | |
| COG | Protein | Clusters of Orthologous Groups of proteins | COG Help Documents | |
| COILS | Protein | Prediction of Coiled Coil Regions in Proteins | COILS Documentation | |
| Dali | Protein | comparing protein structures in 3D | Dali Help | Dali example |
| Jpred | Protein | protein secondary structure prediction | Jpred FAQ | |
| Meme | Protein | Meme protein motif discovery tool | Meme release notes | |
| MetaFam | Protein | Minnesota Protein Metafamily Database | Metafam Description & Demo | Metafam Description & Demo |
| MMDB | Protein | Molecular Modelling Database | MMDB help | |
| Pfam | Protein | Pfam INRA mirror | Pfam information page | |
| Pfam | Protein | Pfam WU mirror | Pfam information page | |
| Pfam | Protein | Pfam Sweden mirror | Pfam information page | |
| Pfam | Protein | database of protein domains and HMMs | Pfam information page | |
| Prodom | Protein | Prodom protein families | | |
| SignalIP | Protein | signal peptide cleavage site prediction | | |
| TMPred | Protein | Prediction of Transmembrane Regions | | |
| TRANSFAC | Protein | Transcription Factor/Protein Binding Sites DB | TRANSFAC Release 4.0 - Documentation | |
| SNP consortium | SNPs | The SNP Consortium | SNP Data Website FAQ | |
| RNA secondary structure prediction | tools | Moscow State U RNA secondary structure prediction | RNA secondary structure prediction | |
| Celera | tools | Celera Corp Public data | Celera FAQ | |
| Clustalw@BCM | tools | BCM Search Launcher: Clustalw Alignment | BCM ClustalW Help (scroll down) | |
| Clustalw@EBI | tools | EBI Clustalw server | ClustalW Help | |
| Jax Lab | tools | Jackson Laboratory: Resources | | |
| mfold server | tools | mfold RNA Structure server, M. Zuker, Rensselaer Polytechnic | RNA Secondary Structure, Lectures by Dr. Michael Zuker | |
| NCBI | tools | NCBI Tools page | NCBI Tools for Datamining | |
| TIGR software | tools | TIGR software | | |
| TRNAscan: WUStL | tools | WUStL tRNAscan SE search tool | User Manual | |
| X2s | tools | UCSC RNA 2ndary structure predictor | Using X2s | |
| 3. Comparative | Type | Website Name | Description, Help info | |
| GMOD | browser | Generic Model Organism Project (GMOD) | GGB: Generic Genome Browser demo | |
| UCSD Genome Browser | browser | UCSD Genome Browser | Human Genome Browser User Guide | |
| CVCGD | Homol | Cardiovascular Comparitive Genomic Database | CVCGD explanation | |
| Hum-Mouse | Homol | Human-Mouse Homology Map | | |
| NIH model organisms links | model orgs | Model Organisms for Biomedical Research (NIH) | | |
| Berkeley Drosophila DB | model orgs | UC Berkeley Drosophila Genome Project | BDGP Information | |
| Ensembl Mouse | model orgs | Ensembl Mouse Genome Server | | |
| Jax Lab | model orgs | Jackson Lab Mouse Genome Informatics | MGD Project | |
| Rat Genome DB | model orgs | Rat Genome Database | About RGD | |
| ZFIN searches | model orgs | Zebra Fish Info Network | The Zebrafish Database Project | |
| Genome Channel | multiple dbs | ORNL Genome Channnel | Genome Channel Users' Guide | |
| Metacyc | metabolic | Karp's Metabolic Pathway database | Metacyc Help | |
| MGD | multiple dbs | Jackson Lab Mouse Genome Informatics | details about MGD | |
| TIGRFAMs | protein | TIGR Protein Families | Terms associated with TIGRFAMs | |
| SCPD | regulation | The Promoter Database of Saccharomyces cerevisiae | Manual for the SCPD Database | SCPD Examplesl |
| Eisenberg protein structure | tools | Eisenberg UCLA Protein Crystallography | | |
| GXD | tools | Jackson Labs' Gene Expression Database | The Gene Expression Information Resource Project | |
| Pipmaker | tools | PIPmaker Percent Identity Plot tool | Pipmaker Help | Pipmaker examples |
| Slam | gene prediction | SLAM Comparative Gene Prediction | Slam Help | Slam Example |
| Trace Archive | tools | NCBI Trace Archive | NCBI Trace Archive Documentation: raw data for 4 vertebrates | |
| 4. Arrays | Type | Website Name | Description, Help info | |
| EBI Expression Profiler | expression | EBI Expression Profiler | Documentation about the tools in Expression Profiler | |
| GEO | expression | NCBI Gene Expression Omnibus | GEO faq | |
| SMD | expression | Stanford Microarray Database | Stanford Microarray Database (SMD) Specifications | |
| MGED | forums | MicroArray Gene Expression Database Group | EBI Microarray Discussion list | |
| SU Microarray Forum | forums | Stanford Microarray software discussion site | Stanford Microarray Forum FAQ | |
| DNA Microarray (Genome Chip) homepage | links | L. Shi's list of microarray links and papers | | |
| EBI Expression and Microarray Links | links | EBI Expression and Microarray Links | | |
| Microarray Databases | multiple dbs | Microarray databases on the WWW: | | |
| Statistics paper | papers | Dudoit, Speed et.al. Microarray Statistics paper | | |
| ArrayMaker Guide | tools | Brown Lab's complete guide to microarraying | Pat Brown's instructions on making a microarray robot | |
| EBI MicroArray Informatics | tools | MicroArray Informatics at the EBI | Large-Scale Gene Expression and Microarray Links and Resources | |
| Eisen Lab DB | tools | Eisen Microarry Lab at LBNL | Example data for ftp download | |
| GeneExplorer | tools | Christian Rees' GeneExplorer | Christian Rees' GeneExplorer based on Eisen's TreeView | GenExplorer Example |
| GenMapp | tools | UCSF Gene Microarray Pathway Finder | | |
| GridIt | tools | VA Tech Resources for Microarray | | |
| PubGene: Arrays | tools | PubGene Expression Data biobibliome search | Offline demo of PubGene GeneExpression Analysis | PubGene Example |
| Stanford Microarray DB | tools | Stanford Microarray DB | SMD Public Microarray data | |
| SU Microarray Analysis Lab | tools | Stanford U Microarray Analysis Lab (Tibshirani) | | |
| TIGR ArrayViewer | tools | TIGR ArrayViewer Info | | |
| TIGR Microarray Tools | tools | TIGR Microarray Tools | "Microarrays in Three Easy Steps" (PDF) | |
| TIGR Spotfinder | tools | TIGR Spotfinder Info | | |
| UCB Microarray Statistics | tools | Speed Group Microarray Software Page | | |
| UCSC microarray SVM | tools | UCSC DNA Microarray Facility | Expression Array results: Support Vector Machine classification | Example Analysis of Alternate Splicing in Human Genes |
| 5. Misc | Type | Website Name | Description, Help info | |
| Bay Genomics Bioinformatics Tutorial | bioinf. Course | Bay Genomics Bioinformatics Tutorial | | |
| Bioinformatics (Genomics) | bioinf. Course | Queens University online Bioinformatics course | | |
| CMBI homology modelling course | bioinf. Course | Center for Molecular and Biomolecular Informatics (Netherlands) | | |
| CSHL 2002 Courses | bioinf. Course | Cold Spring Harbor Lab Courses, 2002 | | |
| CSHL Course 10/2000 | bioinf. Course | CSHL Computational Genomics Course 10/2000 | see esp. the Exercise pages | |
| Dr. Brian Steipe's bioinformatics lecture notes | bioinf. Course | University of Munich bioinformatic lecture notes | | |
| Genefinding (Short Overview) | bioinf. Course | Genome Informatics Research Lab (Spain) | | |
| GenomeWeb list of Bioinformatics Intros | bioinf. Course | GenomeWeb Introductions to Bioinformatics | | |
| HGMP Bioinformatics 3-day course outline | bioinf. Course | HGMP Bioinformatics 3-day course | | |
| Human genome: advanced annotation tutorial | bioinf. Course | Mad-cow.org Annotation tutorial | | |
| Manchester Bioinformatics online | bioinf. Course | Theory and Applications in Bioinformatics (U Manchester distance learning) | | |
| Online Lectures on Bioinformatics | bioinf. Course | Martin Vingon's online Bioinformatics course | | |
| SACS Bioinformatics Seminars | bioinf. Course | UCSF Sequence Analysis & Consulting Service Seminars | | |
| S-Star GLOBULE | bioinf. Course | S-Star consortium streaming video bioinformatics courses | | |
| TIGR/Jax Lab PGA Workshop | bioinf. Course | Gene Microarray Development & Analysis | | |
| UCSD Bioinf course | bioinf. Course | UCSD Bioinformatics course outline, BIMM100 | | |
| US Bioinformatics courses | bioinf. Course | University Bioinformatics Programs (U Texas list) | | |
| Weizmann Institute Bioinformatics | bioinf. Course | BIOINFORMATICS and COMPUTATIONAL GENOMICS COURSES at WIS | | |
| Stanford Computational Molecular Biology | bioinf. Course | Stanford Computational Molecular Biology | | |
| DOE ELSI program | ELSI | DOE ELSI program | | |
| LBNL ELSI website | ELSI | LBNL ELSI website | | |
| NHGRI ELSI program | ELSI | NHGRI ELSI program | | |
| BMC Bioinforrmatics online journal | journal | Biomedical Center Bioinformatics online journal | | |
| PubGene: Biobibliome search | Lit. search | PubGene: Biobibliome search | Offline demo of PubGene Network Browser | |
| BayGenomics ES Database | other PGAs | BayGenomics ES Database | | |
| NHLBI PGAs list | other PGAs | NHLBI Programs for Genomic Applications | | |
| Genome Glossary | reference | A glossary of genetic terms from the DOE Human Genome Program | | |
| 123Genomics resource list | resource list | Learn about Bioinformatics, Proteomics, Genomics, Microarrays, etc. | | |
| BayGenomics resource list | resource list | Bay Genomics Useful Web Resources | | |
| Bioinformatik resources | resource list | list of online bioinformatic training materials | | |
| Human Genome Central | resource list | Ensembl Human Genome Central | | |
| ISCB list of bioinformatics courses | resource list | Int'l Society for Computational Biology list | | |
| NBI list of Bioinformatics courses | resource list | National Bioinformatics Institute Education resources list | | |
| RU Bioinformatics course list | resource list | Bioinformatics courses worldwide (Rockefeller U.) | | |
| TBR-the Bioinformatics Resource | resource list | HGMP Bioinformatics Resource site | | |
| Aix U. list of online analysis tools | tool list | Aix U. list of online analysis tools | | |
| "Exploring our Molecular Selves" | Genome Education | NHGRI Multimedia Kit | | |
| Genome Education Center | Genome Education | U. Kansas Medical Center Education page | | |
| HGMIS Education links | Genome Education | HGMIS Education links | | |