| 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 |
|
| 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 |
|
| 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 |
|
| 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 |
|
| 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 |
|
| 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 |
|
| 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 |
|
| 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 |
|
|
