Bioinformatics Workshop Tools and Websites

This table lists many useful bioinformatics tools and web sites.

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 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 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
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

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