• Africa - ancient to present day including many cultural aspects over 50 links  (see also Unit 6 - Global Perspectives)
• American History - early colonial, civil war, reconstruction, world wars to present day many cultural reference over 250 links
• American Indians - covers many tribes and eras over 100 links
• Ancient Civilizations- Fertile Crescent, Egypt, Greece, Rome, Kiev, China, India, Mayans, Aztec, as well as concepts for civilization well over 350 links (see also Unit 1 - Pre-historym Ancient & Classical Civilizations)
• Archeology & Anthropology - over 15 links
• Arts & Humanities - 15 links to art in different ages, eras and places
• Asia & India - China, Japan, India, Korea and more covers time, place, events, cultural references such as clothing, samuri, over 125 links (see also Unit 6 - Global Perspectives)
• Block scheduling issues - articles and data on successes and failures of the block system over 40 links
• Bosnia & Balkans - past and present history, cultural references, NATO and US involvement, current events, ethnic cleansing over 50 links
• Central  & Meso - America - Links to history and culture on Mexico, Panama, Aztec, Mayan, and other ancient civilizations plus colonial history, revolutions and people over 75 links
• College - over 50 links to college net, national & state colleges, SAT, GRE, College rankings, College Board, college mascots, sports, nicknames, financial aid
• Costumes - 30 - 40 of the best sites on the web for eras and place
• Dictators - links to historical and contemporary dictators. (see also Unit 5 - 2oth Century)
• Economics - 15 - 20 links to theory, stock market, quotes, history of Dow Jones,  IRS, timeline of economists,
• Europe  (Germany, Italy, Russia, France, Great Britain, etc..)  between 200 - 225 links different eras
• Flags and Anthems- links to US & World flags.  Includes historical flags. Some military flags. Crests of Monarchs.  State songs and some National Anthem links.  Over 50 links.
• General Education - learning issues plus resources for special education, evaluation tools, data from orgainizations, Educational ogranizations, curriculum tools, TAAS , GRE, TEA, NCSS,  ESL, IB etc..It's full of all these letters over 50 sites
• Geography - 40 -50 links to latitude, longitude, volcano, weather, Atlas,  supulatives (highest, most etc..)
• Government -  over 50 links Consitutional  issues and documents, political theory, offical governent sites
• Holocaust - about 30 links but more coming including an interactive for research at this site (see also Unit 5 - 20th Centuiry)
• Literature - under construction but some links divided by historical era
• Maps-  over  50 sites of hard to find maps historical maps from ancient civilizations to present day
• Math - under construction but already 10 -15 links including biographies of mathematicians. Great new site that has applets.
• Middle Ages - castles, feudalism, monarchs, crusades and more.  Over 300 links (under construction) being separated from Renaissance links below
• Middle Ages & Renaissance - European, African, Asian, etc... castles, art, maps, people between 400 -450 links (see also Unit 2 - Middle Ages and Renaissance)
• Middle East - a couple of links that deal with history and current events, names places
• News Sources for current events - newspapers, newsprograms, magazines between 30 - 40 great sources
• Reference- dictionaries, encyclopedias between 30 - 40 sites
• Research Resources - 75- 100 resources on the web for data collection
• Revolution - American, French, Russian, English, Mexican and more between 50 - 100 links (Unit 3 - Revolutions)
• South America - links to ancient civilizations plus listing of Countries in South America and revolutions and other history
• Technology - over 25 sites web technology, web hosting sites, science and inventions issues, patten issues
• Terrorism - over 50 links  (see also Unit 6 - Global Perspectives)
• Texas History - 50 - 60 links to songs of Texas, government organizations, seal, bird, tree, bird. State government links to officials and agnecies
• Victorian Era -  events and culture during the 1800s includes literary works of Dickens between 50 - 100 links (Unit 4 - Victorian Era - 1800s)
• Women in History - over 30 links to general sites during specific eras and to individual biographies of women in history
• World History - general resources between 150 - 200 links

• DNA/PROTEIN DATABASES
  • GENERAL DATABASE INFO
  • SEQUENCE SUBMISSION
    • Vector screening
  • SEQUENCE RETRIEVAL
  • ALERT SERVERS
  • GENOMICS
    • GENERAL GENOMICS
    • HUMAN GENOME PROJECT
    • OTHER GENOME PROJECTS
    • COMPARATIVE GENOMICS
    • COMPLETE GENOMES AND GENOME PROJECTS
    • PARASITE GENOME PROJECTS
• TAXONOMY
  • RIBOSOMAL RNA
• DNA SEQUENCE ANALYSIS
  • GENE PREDICTION
  • TRANSLATION
  • ORF ANALYSIS
  • TRANSCRIPTION FACTOR BINDING SITES
  • REPEATS
  • CODON USAGE
  • PATTERN SCAN
  • CONTIG ASSEMBLY
  • RESTRICTION ENZYME
    • RE ANALYSIS
    • RE LISTS
  • OLIGO/PRIMER ANALYSIS
  • SIMPLE NUCLEOTIDE MANIPULATIONS
• PROTEIN SEQUENCE ANALYSIS
  • AMINO ACID/PROTEIN INFORMATION
  • HYDROPHOBICITY PLOT
  • REVERSE TRANSLATION
  • MOTIFS / PATTERNS SEARCHING
  • GENEQUIZ
  • PREDICTPROTEIN
  • DARWIN
  • STATISTICAL ANALYIS
  • DIGESTION PRODUCTS SEARCH
  • PROTEIN SORTING / LOCALIZATION
  • ISO-ELECTRIC POINT / MOLECULAR WEIGHT
  • AMINO ACID COMPOSITION
• SEQUENCE ALIGNMENT
  • SEQUENCE-FORMAT CONVERSION
  • PAIRWISE SEQUENCE ALIGNMENT
  • MULTIPLE SEQUENCE ALIGNMENT
    • ALIGNMENT VISUALISATION/EDITING/FORMATTING
• SEQUENCE HOMOLOGY SEARCHES
  • BLAST
  • FASTA
  • SW (Smith-Waterman)
  • BASED ON AA COMPOSITION
  • DARWIN
• SECONDARY/TERTIARY STRUCTURE PREDICTION
  • RNA
  • PROTEIN
• PHYLOGENY
• MEDLINE
• 3D PROTEIN IMAGES
  • Protein Database Brookhaven PDB
  • CHIME 3D
• METABOLIC PATHWAYS
• GENERAL BIOINFORMATICS SITES
  • SEQUENCE ANALYSIS TOOLS
  • CMS-SDSC MOLECULAR BIOLOGY RESOURCE
  • PEDRO'S BIOMOLECULAR RESEARCH TOOLS
• TUTORIALS AND COURSES ON THE WEB
• SOFTWARE FOR SEQUENCE ANALYSIS

DNA/PROTEIN DATABASES

GENERAL DATABASE INFO

• Database Statistics (courtesy of DDBJ)
• Human Genome Sequencing
• GENBANK (NCBI)
• GENBANK SITEMAP
• EMBL (EBI)
• PDB Protein 3D database
• Nucleotide sequences at EBI
• Nucleotide sequences at GenBank
• MAGPIE - Multipurpose Automated Genome Project Investigation Environment
• DDBJ (DNA Data Bank of Japan)
• MBGD Microbial Genome Database
• HOX Pro DataBase (in Russia)
• HOX Pro DataBase (Mirror in the US)
• Expasy Home of SwissProt Protein database
• SWISS-PROT (ExPasy)
• The Sanger Centre
• Genome Monitoring Table (daily update EBI)
• MAGPIE
• NIH News Release 06/26/2000
• Enzyme Nomenclature
• TIGR Microbial Database
• Pfam Protein domain database at Sanger Centre
• The TIGR Trypanosoma brucei Database
• Trypanosome GeneDB at Sanger
• BMERC Completed Genomes collected resources
• DNA Sequence Collaborator's Page
• Genome Sequence Database GSDB (NCGR)
• PEDANT complete genome analysis
• C. elegans Database
• The Protein Research Foundation
• Population studies with PopSet with aligned DNA seqiences
• Extinct organisms in GenBank
• DBGET Database Document: GenBank

SEQUENCE SUBMISSION

• GENBANK BankIt
• GENBANK Sequin
• EMBL Webin
• DDBJ Sakura
  
  Vector screening
  • VecScreen (NCBI)
  • Vector Scanning (EBI)
  • Vector Screening System (DDBJ)
    

SEQUENCE RETRIEVAL

DNA

• ENTREZ-Nucleotide query (NCBI)
• SRS at EMBL-EBI, Hinxton (UK)
• DNA Search (GenomeNet, Japan)
• GENBANK at NCBI
• Direct retrieval from EMBL via accession code
  
  PROTEIN
  
• ENTREZ-Protein query (NCBI)
• SRS at EMBL-EBI, Hinxton (UK)
• Protein Search (GenomeNet, Japan)
• SWISS-PROT and TrEMBL (Switzerland)
• RCSB Protein Data Bank (US)
• RCSB PDB Mirror Sites
• PIR-Web - The Protein Identification Resource (NONACTIVE)
• GENBANK using ENTREZ
• Protein Search (GenomeNet, Japan)
• Direct retrieval from EMBL via accession code

ALERT SERVERS

• EMBL Sequence Alerting System
• SWISSPROT alert server
• BEN sequence awareness service (registered users only)
• BEN sequence similarity awareness service (registered users only)
  

GENOMICS

GENERAL GENOMICS

• Entrez-Genome (NCBI)
• Genome Monitoring Table (daily update EBI)
• NCGR National Center for Genome Resources
• Genome Channel (Oak Ridge, US) *
• Organism-specific Databases
• GOLD: Genomes OnLine Database Homepage
• PEDANT front page
• NIH News Release 06/26/2000
• The Human Genome, by All of the Top Cartoonists

HUMAN GENOME PROJECT

NIH/NCBI HUMAN GENOME RESOURCES

• The Human Genome
• Entrez Genome view: MAPVIEWER
• LocusLink Introduction
• Human Genome Sequencing
• National Human Genome Research Institute (NHGRI)
• dbSNP Home Page
• NCBI Contig Build and Annotation Process

ENSEMBL (EBI/Sanger Institute)

• Ensembl Genome Server (not active)

HUGO (Human Genome Organisation)

• HUGO homepage
• HUGO human chromosomes page
• HUGO Gene Nomenclature Committee (HGNC)

OMIM (Online Mendelian Inheritance in Man)

• OMIM - Online Mendelian Inheritance in Man

GENECARDS

• GeneCards (Weizmann Institute, Israel)
• GeneCards mirror (Finland)
• GeneCards mirror (Germany)
• GeneCards mirror (Canada)
• GeneCards mirror (Japan)

DDBJ/CIB HUMAN GENOMICS STUDIO

• DDBJ/CIB Human Genomics Studio

HGSC Human Genome Sequencing Center (Baylor College of Medicine)

• Welcome to Baylor HGSC

ONL Oak Ridge National Laboratory

• Human Genome Landmarks Poster
• Human Genome Project Information

ETHICAL, LEGAL, SOCIAL ASPECTS

• Clinical and patient aspects (HUGO)
• Ethical, Legal and Social Implications (ELSI; NHGRI at NIH)

OTHER GENOME PROJECTS

EUKARYOTIC GENOME PROJECTS

• Mouse Genome Resources Page
• Rat Genome Resources Page
• Zebrafish Genome Resources Page
• Drosophila melanogaster @ NCBI
• Malaria Genetics & Genomics
• C. elegans project
• Arabidopsis thaliana

PARASITE GENOME PROJECTS

• Trypanosoma brucei Genome Project
• Leishmania Genome Network
• Trypanosoma brucei home page (at Sanger)
• Trypanosoma brucei Genome Network home page
• Trypanosoma brucei GSS sequences for downloading
• The TIGR Trypanosoma brucei Database
• Trypanosome GeneDB at Sanger
• Trypanosoma cruzi Blast search at TIGR
• Leishmania major home page (at Sanger)
• Leishmania Genome Network home page
• Leishmania major chromosome 15
• Leishmania major chromosome 26
• Leishmania major chromosme 28
• Leishmania Genome Network, Seattle, USA
• Parasite-genome database at EBI
• Parasite genome Blast server at EBI
• Parasite genomes databasesWHO Leishmania Genome Network Web site
• Malaria (Plasmodium falciparum genome map)
• Plasmo DB (Plasmodium Genome database)

MICROBIAL GENOME PROJECTS

• PEDANT complete genomes
• Entrez: microbial genomes taxonomy tree
• TIGR Microbial Database
• DDBJ Genome Information Broker

VIRAL GENOME PROJECTS

• Complete viral genomes (NCBI)
• Retroviruses

COMPARATIVE GENOMICS

• PEDANT CrossGenome categories
• COG: Clusters of Orthologous Groups of proteins( NCBI)
• TaxPlot (NCBI)
• HOBACGEN Homologous Bacterial Genes Database
• WIT Home Page
• KEGG Kyoto Encyclopedia of Genes and Genomes
• ERGO (Integrated Genomics, Inc.)
• LION bioscience | Products and Services | genomeSCOUTú

COMPLETE GENOMES AND GENOME PROJECTS

• GOLD Genome On line Database
• Proteome analysis at EBI
• All Available Complete Genomes
• GeneQuiz (Genome annotations)
• LocusLink (Human, Mouse and Rat Loci)
• Entrez Genomes Views (Human Chromosomes)
• Mitochondrial Genomes Database
• GOBASE - The Organelle Genome Database
• Saccharomyces Genome Database
• Mycoplasma genitalium database (not available)
• Haemophilus influenzae database (not available)
• Methanococcus jannaschii database (not available)
• E. coli genome center
• Heliobacter pylori database (not available)
• E. coli database collection (not available)
• Sanger Center C. elegans homepage (not available)
• Bacillus subtilis database
• Genome Sequencing Center, St. Louis
• Methanobacterium thermoautotrophicum abstract
• The Genome Database
• Sanger Center S. pombe homepage (not available)
• Human Genome Project Infor
• Mouse Genome Databasemation (not available)
• Arabidopsis thalianaProject
• Arabidopsis genome completed (Nature paper, 2000)
• Flybase(not available)
• Drosophila database
• TIGR Arabidopsis thaliana Database
• TIGR Archaeoglobus fulgidus Database(not available)
• TIGR Borrelia burgdorferi Database(not available)
• Pyrococcus furiosus news article
• Pyrobaculum aerophilum abstract(not available)
• Sulfolobus solfataricus P2 complete genome
• Borrelia burgdorferi news article
• Yersinia Pestis complete genome
• HOBACGEN (the Homologous Bacterial Genes Database)

TAXONOMY

• NCBI Taxonomy Homepage
• Taxonomy Browser at NCBI
• The Tree of Life Home Page
• Introduction to Phylogeny

  RIBOSOMAL RNA

  • Ribosomal Database Project II (USA)
  • The rRNA WWW Server (UIA Antwerp)

DNA SEQUENCE ANALYSIS

GENE PREDICTION

• EMBOSS at EBI
• Gene Finder at Sanger centre
• PredictGenes (Darwin) (Switzerland)
• SBDS sequence analysis
• Bipartite Nuclear Localisation Sequence Locator
• IUPAC-IUB Abbreviations and symbols for nucleic acids, polynucleotides and their constituents.
• GENSCAN at MIT (US) ***
• WebGeneMark
• GrailEXP at Oak Ridge (US)
• Genie at Berkeley (US)
• Gene Prediction Services

  TRANSLATION

• EMBOSS at EBI
• ExPASy - Translate tool
• DNA Sequence Translation (ALCES)
• The Protein Machine (EBI)
• Nucleic Acid to Amino Acid Translation (London)
• Nucleic Acid to Amino Acid Translation (London - mirror)
• SeWeR is a DHTML interface for web based sequence analysis
• IUBMB Prokaryotic and eukaryotic translation factors.

ORF ANALYSIS

• EMBOSS at EBI
• ORF Finder (NCBI)
• ORF analysis (WebGene)
• FGENESH-2 Improving gene finding accuracy
• FGENESH HMM - Gene finding for mouse genes

TRANSCRIPTION FACTOR BINDING SITES

• TFSEARCH: Searching Transcription Factor Binding Sites
• MatInspector (Germany)
• Alibaba2 (Germany)

REPEATS

• EMBOSS at EBI
• Dot Plot Analysis THEORETICAL EXPLANATION
• Dot Plots (Colorado State University) (limit: 20.391bp x 20.391 bp)
• Dot Plot (to itself) (ALCES) (postscript/GIF output)
• Blast 2 Sequences (NCBI)

CODON USAGE

• Codon Usage Database
• Codon usage (ALCES)

CONTIG ASSEMBLY

• CAP sequence assembly at Infobiogen
• CAP Sequence Assembly at BCM Search Launcher

PATTERN SCAN