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