DNA > Genome Resources
Quick Data: UniGene, Nucleotide/Protein sequences, 3D Structure, Genomes, OMIM, PubMed at NCBI

Genome Resources List- Human - Yeast - Worm - Fly - Zebrafish - Fugu - Mouse - Rat - Chicken - Dog - Cat - Cow - Chimpanzee

*GOLD[TM]: Genomes OnLine Database v. 2.0 (Liolios et al., 2006)   |  Complete Genome Tracking Database (COGENT)
*Integr8 and Genome Reviews - integrated views of complete genomes and proteomes (Kersey et al., 2005)
PartiGeneDB - collating partial genomes (Peregrin-Alvarez et al., 2005)
TIGR Gene Indices   |   Genomes Projects at Baylor College of Medicine   |  Genome monitoring table at EBI
Animal Genomics: Cytogenet Genome Res Vol. 102, No. 1-4, 2003
The Vertebrate Genome Annotation (Vega) database (Ashurst et al., 2005)
Inparanoid - a comprehensive database of eukaryotic orthologs (O'Brien et al., 2005)

Human Genome Databases - Human chromosomes

Human gene number wager won: Geneticists draw sweepstake despite uncertainty over final tally
A Low Number Wins the GeneSweep Pool
Vertebrate genome sequencing: building a backbone for comparative genomics <>MAIN SITES
National Human Genome Research Institute (NHGRI) (the reference Center for the Human Genome Project)
The Sanger Centre - Human Genome Project
***GENOME BROWSER at UCSC (Karolchik et al., 2004; Hinrichs et al., 2006) - Proteome Browser (Hsu et al., 2005)
***Homo sapiens Map Viewer  at NCBI - Human Genome Resources: Sequencing  |  Clone Registry
***Ensembl Server (Birney et al., 2004, 2006; Hubbard et al., 2005)
***<>1000 Genomes

Genome Function:
Encode Explorer

General organization of the Human genome (by Strachan)
USER'S GUIDE TO THE HUMAN GENOME   |   Nature Human Genome Collection
***Nature - Genome Information Centre - The Human Genome | Working Draft | CD: Education kit at NHGRI
***Nature ENCODE 2012
***Science - Genome Landmarks - Functional Genomics - The Human Genome Special Issue
***Celera - Celera Publication Site
***Diploid Genome Sequence of an Individual Human - PLoS Biology, Sep 4, 2007 - HuRef - Sequences
***Genomebiology -"A draft annotation and overview of the human genome" - 70,000 estimated transcription units
***Revisiting the independence of the publicly and privately funded drafts of the human genome:
***Cozzarelli, Waterston et al., Adams et al. on PNAS, March 11, 2003
***Genomics website at Wiley - Physiological Genomics
***Human Genome Project Information and Human Genome Project Publications
News: Human Genome News Chronological Archive   |  NIH VideoCasting: Genome Analysis - Human Genome Lecture Series
Human genome: End of the beginning - Nature, Oct 21, 2004
High Throughput Genomic Sequences   -   HTG: publication
Human Gene Nomenclature  - Database (Wain et al., 2004; Eyre et al., 2006)
Guidelines for Human Gene Nomenclature (2001) - Nomen at Nat. Genet.
  • BLAST Human Genome
  • Genome Data Base - Home Page  -  Search - Find a gene
  • Unigene-Homo sapiens
  • HAGR - the Human Ageing Genomic Resources (de Magalhaes et al., 2005)

  • Segmental duplications - Paralogy
  • Segmental duplication DB
  • Genome-wide detection of segmental duplications - GenomeBiology, March 2003
  • FISH 1.0 - Fast Identification of Segmental Homology - Jul 30, 2003
  • GenDiS - Genomic Distribution of protein structural domain Superfamilies (Pugalenthi et al., 2005)

  • The Sanger Centre: 1998 Gene Map - RH Server
  • Cancer Chromosome Aberration Maps (CCAP) at NCI
  • HCAD - closing the gap between breakpoints and genes (Hoffmann et al., 2005)
  • BCM clones data
  • Human mitochondrial DNA (MITOMAP)
  • ActionMap - loci assignments to framework maps (Albini et al., 2003)

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    Human Chromosome 1
    The Sanger Centre: Human Chromosome 1HC1 BLAST server | Chr. 1 workshop
    GeneMap99: Chr.1
    Genes on Chromosome 1 at GDB

    Human Chromosome 6
    The Sanger Centre: Human Chromosome 6HC6 BLAST server
    GeneMap99: Chr.6
    Genes on Chromosome 6 at GDB

    Human Chromosome 21
    Human Chromosome 21 home at RIKEN
    CroW 21 - integrated data related to human chromosome 21 - joining the chromosome 21 specific databases
    CSMC Molecular Genetics   (Laboratory of Julie Korenberg - Chromosome 21 Mapping)
    Research Laboratories of Medical Genetics of the University of Geneva (Laboratory of S.E. Antonarakis)
    GeneMap99: Chr.21
    Genes on Chromosome 21 at GDB - Human Chromosome 21 cSNP Database and MAP
    JST Human Genome Sequencing Home Page - Chromosome: 21
    Human Chromosome 21 Launchpad
    Sites of interest to human chromosome 21
    MOUSE CHROMOSOME 16 at Celera
    Human Chromosome 21 gene expression "atlas"
    HumanGenomeSequencing Centers
    Foundation for Genetic Medicine, Inc.
    The Wellcome Trust Centre for Human Genetics
    Whitehead Institute/MIT Genome - Sequencing Project
    Genome Sequencing Center - WashU
    Cooperative Human Linkage Center
    BCM Sequencing
    Lipper Center for Computational Genetics (Church Lab; Genome/Transcriptome/Proteome/Physiome/Biome)

    Genome Databases List- Human - Yeast - Worm - Fly - Zebrafish - Fugu - Mouse - Cow

    Saccharomyces Genome Database   |   MIPS Comprehensive Yeast Genome Database (CYGD) (Guldener et al., 2005)
    Fungal BLAST and Model Organism BLASTP Best Hits - new comparison resources at the SGD (Balakrishnan et al., 2005)
    The Yeast Resource Center Public Data Repository (Riffle et al., 2005)
    YETI - Yeast Exploration Tool Integrator (Orton et al., 2004)
    The Sanger Centre: S. pombe Blast server
    Yeast at WWW Virtual Library

    FlyBase - A Database of the Drosophila Genome - FlyBase: genes and gene models (Drysdale et al., 2005; Grumbling et al., 2006)
    Drosophila Melanogaster @ NCBI
    FlyEx - A Database of Segmentation Gene Expression in Drosophila

    Wormbase- a comprehensive data resource for Caenorhabditis biology and genomics (Harris et al., 2004; Chen et al., 2005)
    C. elegans movies
    C. elegans II - 1997, Cold Spring Harbor Laboratory Press
    The Worm in Us: Caenorhabditis elegans Models of Human Diseases (Baumeister and Ge, 2002)
    The Sanger Centre: C.elegans Blast server
    The Intronerator - exploring introns and alternative splicing in Caenorhabditis elegans (Kent and Zahler, 2000)
    Comparative genomics: Two worms are better than one - Nature, 2003
  • Caenorhabditis elegans Genetics and Genomics
  • Caenorhabditis elegans WWW Server - Worm Literature Index
  • The Original CPC: Comprehensive Worm Protocol Collection
  • C elegans Labs

    Fish Genomics - special number of Gene, August 2002
    Developmental Dynamics - Special Issue: Zebrafish
    The Zebrafish Information Network (Sprague et al., 2006) and Server   |  Zebrafish newsgroup at BIOSCI - Zebrafish FAQS
    Unigene: Danio Rerio   |   The Danio rerio Sequencing Project at Sanger Center
    Zebrafish Genome Resources at NCBI   |  Blast The Zebrafish Genome
    The Syntenic Relationship of the Zebrafish and Human Genomes (Barbazuk et al., 2000)
    Morpholino oligos   at Gene Tools   |   The Stainier Lab at UC San Francisco   |  ZF-MODELS (European Commission Project)
    (Ita - Bologna) Sperimentazione su animali

    HGMP Resource Centre FUGU Project
    Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes - Aparicio et al., Science, July 25, 2002

    Initial sequencing and comparative analysis of the mouse genome - Nature, December 2002
    The Mouse Genome Database (MGD) - from genes to mice--a community resource for mouse biology (Eppig et al., 2005, Blake et al., 2006)
    The Mouse Functional Genome Database (MfunGD) - functional annotation of proteins in the light of their cellular context (Ruepp et al., 2006)
    MGD: Genetic and Phenotypic Data Menu
    Unigene: Mus musculus
    Mus musculus Genome Resources Pages at NCBI
    The Mouse Genome Informatics Mouse BLAST Server
    Mouse Gene Expression at MGI
    WI/MIT Mouse Radiation Hybrid Mapper
    An analysis of 2,820orthologous rodent and human sequences - by Makalowski and Boguski
    Knockout Mice Database

    The rat genome - Nature, April 1, 2004
    Rat genome resources   |   Unigene: Rattus Norvegicus
    The Rat Genome Database (RGD) - developments towards a phenome database (de la Cruz et al., 2005)
    RatMap--rat genome tools and data (Petersen et al., 2005)

    Nature web focus: The Chicken Genome
    Transcriptome analysis for the chicken (Hubbard et al., 2005)
    ChickVD - a sequence variation database for the chicken genome (Wang et al., 2005)

    Unigene: Canis familiaris
    Genome sequence, comparative analysis and haplotype structure of the domestic dog  (Nature, 2005)

    Initial sequence and comparative analysis of the cat genome (Pontius et al., Genome Research, 2007)

    Unigene: Bos Taurus

    Nature web focus: The chimpanzee genome
    Chimp genome (Nature)


    Poxvirus Bioinformatics Resource Center - a comprehensive Poxviridae informational and analytical resource (Lefkowitz et al., 2005)
    BacMap - an interactive picture atlas of annotated bacterial genomes (Stothard et al., 2005)
    Metagrowth - a new resource for the building of metabolic hypotheses in microbiology (Ogata and Claverie, 2005)
    VFDB - a reference database for bacterial virulence factors (Chen et al., 2005)
    EchoBASE - an integrated post-genomic database for Escherichia coli (Misra et al., 2005)
    EcoCyc - a comprehensive database resource for Escherichia coli (Keseler et al., 2005)
    Pseudomonas aeruginosa Genome Database and PseudoCAP - community-based genome annotation (Winsor et al., 2005)
    The Diatom EST Database (Maheswari et al., 2005)
    The Ashbya Genome Database (AGD) - a tool for the yeast community and genome biologists (Hermida et al., 2005)
    CandidaDB - a genome database for Candida albicans pathogenomics (d'Enfert et al., 2005)
    The Candida Genome Database (CGD) - a community resource for Candida albicans gene and protein information (Arnaud et al., 2005)
    PROPHECY - a database for high-resolution phenomics (Fernandez-Ricaud et al., 2005)
    MDS_IES_DB - a database of macronuclear and micronuclear genes in spirotrichous ciliates (Cavalcanti et al., 2005)
    Plasmodium Falciparum
    openSputnik--a database to ESTablish comparative plant genomics (Rudd, 2005)
    PlantMarkers--a database of predicted molecular markers from plants (Rudd et al., 2005)
    The Arabidopsis Information Resource -
    Arabidopsis nucleolar protein database (AtNoPDB) (Brown et al., 2005)
    ASRP - the Arabidopsis Small RNA Project Database (Gustafson et al., 2005)
    GeneFarm - annotation of Arabidopsis gene and protein families by a network of experts (Aubourg et al., 2005)
    RARGE - a large-scale database of RIKEN Arabidopsis resources (Sakurai et al., 2005)
    CR-EST - a resource for crop ESTs (Kunne et al., 2005)
    Rice Annotation Database (RAD) - a contig-oriented database for map-based rice genomics (Ito et al., 2005)
    Brassica ASTRA - an integrated database for Brassica genomic research (Love et al., 2005)
    The Legume Information System (LIS) - comparative legume biology (Gonzales et al., 2005)
    PoMaMo--a comprehensive database for potato genome data (Meyer et al., 2005)
    The Mosquito Genome: Anopheles gambiae
    SilkDB - a knowledgebase for silkworm biology and genomics (Wang et al., 2005)
    SilkSatDb - a microsatellite database of the silkworm, Bombyx mori (Prasad, et al., 2005)

    c-value paradox
    Genome sizes discussion
    Genome size of Medakafish - one-half of the zebrafish genome, two times of the pufferfish genome.

    Last updated January 04, 2013