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Genomes

Genomes. School B&I TCD Bioinformatics May 2010. Genome sizes. Completed eukaryotic nuclear genomes Type of organism Species Genome size (10 6 base pairs) Primitive microsporidian E. cuniculi 2.5 Fungi S. cerevisiae 12.1 Sc. pombe 13.8 N. crassa 40

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Genomes

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  1. Genomes School B&I TCD Bioinformatics May 2010

  2. Genome sizes Completed eukaryotic nuclear genomes Type of organism Species Genome size (106 base pairs) Primitive microsporidian E. cuniculi 2.5 Fungi S. cerevisiae 12.1 Sc. pombe 13.8 N. crassa 40 Nematode worm C. elegans 100 Insect: Fruit fly D. melanogaster 180 mosquito A. gambiae 278 Malarial parasite P. falciparum 22.8 Plants: Thale cress A. thaliana 116.8 rice O. sativa 400 Human H. sapiens 3400 Mouse M. musculus 3454 Rat R. norvegicus 2556 Chicken G. gallus 1200

  3. What’s it all about? • With complete chromosome or big chunks • Can put genes in context, synteny, neighbours • With complete genome • Have all paralogs of gene family • So can identify orthologs – genes similar by descent and so by function • Gene clusters • Operons or “operons” • Tissue expression • Positive selection / excessively variable regions

  4. Caron Human Genome Highly expressed genes are clustered (densely)

  5. Tissue expression mammals

  6. Where are tissue expressed genes clustered?

  7. Mouse/Human Synteny

  8. Three resources • Golden Path at UCSC • Jim Kent and his group at Santa Cruz • Ensembl • Ewan Birney, Wellcome Trust, EBI, Sanger • NCBI Genome Database • US government

  9. UCSC Golden Path • Access to human, mouse, rat, chicken etc. • Two modes: • BLAT search • BLAT search - find sequences of >95% similarity and length >40 bases on the genome. • Genome browser • Choose and display data you want: repeats, SNPs, ESTs

  10. Vertebrate genomes available Human Chimp Rhesus Dog Cow Mouse Rat Cat Opossum Chicken Xenopus Zebrafish Tetraodon Fugu Golden Path UCSC

  11. Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on eukaryotic genomes. • Continually updated and improved.

  12. Mammals Homo sapiens Pan troglodytes (chimp) Macacca mulatto (monkey) Mus musculus (mouse) Rattus norvegicus (rat) Oryctylagus cuniculus (rabbit) Canis familiaris (dog) Bos taurus (cow) Dasypus novemcinctus (armadillo) Loxodonta africana (elephant) Echinops telfari (tenrec) Monodelphis domestica (opossum) … and others Not mammals Gallus gallus (chicken) Xenopus tropicalis (frog) Danio rerio (zebra fish) Tetraodon nigroviridis (puffer fish) Ciona intestinalis (chordate) Drosophila melanogaster (fly) Anopheles gambiae (mosquito) Aedes aegypti (mosquito 2) Apis mellifera (bee) Caenorhabditis elegans (worm) Saccharomyces cerevisiae Ensembl genomes

  13. NCBI Genome Center • Start here for any genome • Bacterial • Archaeal • Eukaryotic • Uniform arrangement of information

  14. NCBI genes and disease • Resource for find authoritative info about diseases. • http://www.ncbi.nlm.nih.gov/books/bookres.fcgi/gnd/tocstatic.html • is one of the many NCBI on-line BOOKS • Classifies diseases and syndromes by • Cancer • Immune system • Muscle and bone • Signals and Transporters • Nervous system • Etc.

  15. OMIM • On line Mendelian Inheritance in Man • Everything you need to know • Diseases and syndromes • But also quirky stuff • But only 2% of syndromes are simple mendelian (single gene)

  16. How to classify genes • What species? • What function? • What gene family • What domains/motifs • What pathway? • What genomic neighborhood/synteny? • What ligands / interactions?

  17. Summary • Different ways/contexts of viewing data • Bioinformatics is integrative biology • Your task is … • To access available resources to maximise our understanding

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