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INTERNET RESOURCES FOR TOPICS PRESENTED IN CHAPTER 1

Domain Names	Electronic Mail & Newsgroups
gTLD-MOU Internet Software Consortium	BIOSCI Newsgroups Eudora Microsoft Exchange NewsWatcher
File Transfer Protocol	Internet Access
Fetch 3.0/Mac LeechFTP/PC	America Online AT&T Bell Atlantic Bell Canada CompuServe Ricochet Telus Worldcom
Virtual Libraries	World Wide Web Browsers
EBI BioCatalog Amos' WWW Links Page NAR Database Collection WWW Virtual Library	Internet Explorer Netscape Navigator
World Wide Web Search Engines	World Wide Web Meta-Search Engines
AltaVista Excite Google HotBot Infoseek Lycos Northern Light	MetaCrawler Savvy Search

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INTERNET RESOURCES FOR TOPICS PRESENTED IN CHAPTER 3

GenBank Release Notes
READSEQ Sequence Conversion Tool
Taxonomy Browser
TREMBL and Swiss-Prot Release Notes

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INTERNET RESOURCES FOR TOPICS PRESENTED IN CHAPTER 4

dbEST dbGSS DDBJ/EMBL/GenBank Feature Table Documentation EMBL Release Notes GenBank Release Notes Genetic codes used in DNA sequence databases

HTGS ORF Finder Taxonomy browser

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INTERNET RESOURCES FOR TOPICS PRESENTED IN CHAPTER 5

BIND Imagemagick mmCif Project National Center for Biotechnology Information (NCBI) NCBI Toolkit

Nucleic Acids Database (NDB) POV-RayAY Protein Data Bank at RCSB RasMol SwissPDB Viewer/Deep View WebMol

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INTERNET RESOURCES FOR TOPICS PRESENTED IN CHAPTER 6

Data Repositories
The Genome DataBase (GDB) National Center for Biotechnology Information Entrez Genomes Division LocusLink GeneMap'99 OMIM HomoloGene	BLAST ePCR Entrez sequence viewer GenBank Genomic Biology page dbSTS Mouse Genome Informatics (MGD/MGI)
Resources & Projects
Cytogenetic BAC LBNL/UCSF RMC U. of Bari Cytogenetic/YAC data NCI CCAP Infobiogen SERGG Coriell ARKdb Animal Genome Database Cedars-Sinai enetic Linkage CEPH Genotype Database CHLC Ge´ne´thon Marshfield MAP-O-MAT Rat Genome Database Radiation Hybrid RHdb RH Information Page Research Genetics WICGR RH Maps WICGR GB4 RH Map Server SHGC RH Maps SHGC G3 Map Server Sanger Centre GB4/GM Map server WICGR human physical map CEPH/Ge´ne´thon YAC map WUGSC home TIGR STCs UWHTSC STCs WUGSC BAC fingerprints	UBGSC mouse BAC fingerprints Trask WICGR mouse physical/genetic map DNA Sequence see NCBI links ORNL Genome Channel Integrated and Catalogs UDB LDB LDB Sequence-based maps eGenome Comparative Mouse Homology Otsuka/Oxford rat-mouse-human Human Chromosome 7-mouse map Bovine Genome Database MCW Rat-Mouse-Human 1 Rutgers 3 UTSA 5 UCI 5 JGI 7 HSC 7 NHGRI 9 UCL 10 GTC 11 Imperial College 16 JGI 19 JGI 21 Colorado 21 RIKEN 21 MPIMG X h Mito Emory HUGO Chromosome resources Sanger Centre

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INTERNET RESOURCES FOR TOPICS PRESENTED IN CHAPTER 7

BLAST Cn3D EndNote Entrez FlyBase GDB GeneCards HomoloGene Kinemage LocusLink

MIPS MMDB OMIM PDB RasMol Reference Manager Sacch3D SGD VAST YPD

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INTERNET RESOURCES FOR TOPICS PRESENTED IN CHAPTER 8

BLAST CLUSTAL W dotter FASTA, lalign hmmer

RepeatMasker seg sim4 Wise package

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INTERNET RESOURCES FOR TOPICS PRESENTED IN CHAPTER 10

Banbury Cross FGENEH GeneID GeneMachine GeneParser GENSCAN Genotator

G RAIL GRAIL-EXP / HMMgene MZEF PROCRUSTES RepeatMasker Sputnik

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INTERNET RESOURCES FOR TOPICS PRESENTED IN CHAPTER 11

Prediction of Physical Properties	Prediction of Protein Identity Based on Composition
Compute pI/MW MOWSE PeptideMass TGREASE SAPS	AACompIdent AACompSim PROPSEARCH
Motifs and Patterns	Prediciton of Secondary Structure and Folding Classes
BLOCKS Pfam PRINTS ProfileScan	nnpredict PredictProtein SOPMA Jpred PSIPRED PREDATOR
Prediction of Specialized Structures or Features	Structure Prediction
COILS MacStripe PHDtopology SignalP TMpred	DALI Bryant-Lawrence FSSP UCLA-DOE SWISS-MODEL TOPITS

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INTERNET RESOURCES FOR TOPICS PRESENTED IN CHAPTER 12

dbEST home page List of dbEST libraries dbEST summary by organism How to submit ESTs to dbEST EST Projects at Washington University The I.M.A.G.E. Consortium UniGene The UniGene build procedure UniGene query engine HomoloGene STACK

TIGR Gene Indices TIGR Orthologous Gene Alignment database GeneMap '98 dbSNP Cancer Genome Anatomy Project (CGAP) CGAP Digital Differential Display (DDD) CGAP xProfiler Serial Analysis of Gene Expression (SAGE) SAGE virtual Northern SAGE xProfiler

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INTERNET RESOURCES FOR TOPICS PRESENTED IN CHAPTER 13

ATQA CAP3 Consed DNASTAR Phrap

Phred Gap4 Sequencher Staden package TIGR Assembler TraceTuner

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INTERNET RESOURCES FOR TOPICS PRESENTED IN CHAPTER 14

Compilation of available phylogeny programs BLAST2 & Orthologue Search CLUSTAL W GeneDoc GeneTree PHYLIP PhyloBLAST

Phylogenetic Resources PUZZLEBOOT ReadSeq RDP Tree TreeView WebPHYLIP

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INTERNET RESOURCES FOR TOPICS PRESENTED IN CHAPTER 15

General	Genome Projects
NCBI EBI ExPASy	GenBank Entrez Genomes division The Institute for Genome Research (TIGR) Microbial Database Integrated Genomics Inc. NHGRI List of Genetic and Genomic Resources The Sanger Centre Washington University-St. Louis Okhlahoma University Microbial Genome Database
Genome Analysis Systems	Databases & Tools for Analysis of Protein Domains
MAGPIE GeneQuiz PEDANT Clusters of Orthologous Groups of Proteins (COGs) Kyoto Encyclopedia of Genes and Genomes (KEGG) What Is There (WIT)	ProDom Pfam SMART Protein modules CDD search
Individual Microbial Genome Databases
Escherichia coli University of Wisconsin-Madison Nara Institute of Technology EcoCyc EcoGene Colibri RegulonDB E. coli Genetic Stock Center (CGSC) Mycoplasma genitalium Mycoplasma genome Essential genes Bacillus subtilis Subtilist Sporulation genes Yeast Saccharomyces Genome Database (SGD) MIPS Yeast Database Yeast Protein Database (YPD) Promoter Database TRIPLES database Cell Cycle Expression Database Metabolic reconstruction Biochemical pathways map ENZYME

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INTERNET RESOURCES FOR TOPICS PRESENTED IN CHAPTER 16

NCBI Databases & Tools	Software
DDD NCBI Gene Expression Omnibus SAGEmap xProfiler	ArrayDB Cluster, TreeView, and ScanAlyze CrazyQuant GeneCluster GeneX ScanAlyze; AMAD

An up-to-date list of the links to laboratories involved in microarray technology development can be found at the NHGRI Web site

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INTERNET RESOURCES FOR TOPICS PRESENTED IN CHAPTER 17

Perl home page
Comprehensive Perl Archive Network
BioPerl

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