Genomes School B&I TCD Bioinformatics May 2010
Genome sizes Completed eukaryotic nuclear genomes Type of organismSpeciesGenome size (10 6 base pairs) Primitive microsporidianE. cuniculi2.5 FungiS. cerevisiae12.1 Sc. pombe13.8 N. crassa40 Nematode wormC. elegans100 Insect: Fruit flyD. melanogaster180 mosquitoA. gambiae278 Malarial parasiteP. falciparum22.8 Plants: Thale cressA. thaliana116.8 riceO. sativa400 HumanH. sapiens3400 MouseM. musculus3454 RatR. norvegicus2556 ChickenG. gallus1200
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
Caron Human Genome Highly expressed genes are clustered (densely)
Tissue expression mammals
Where are tissue expressed genes clustered?
Mouse/Human Synteny
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
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
Golden Path UCSC Vertebrate genomes available Human Chimp Rhesus Dog Cow Mouse Rat Cat Opossum Chicken Xenopus Zebrafish Tetraodon Fugu
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.
Ensembl genomes 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
NCBI Genome Center Start here for any genome –Bacterial –Archaeal –Eukaryotic Uniform arrangement of information
NCBI genes and disease Resource for find authoritative info about diseases. 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.
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)
How to classify genes What species? What function? –What gene family –What domains/motifs What pathway? What genomic neighborhood/synteny? What ligands / interactions?
Summary Different ways/contexts of viewing data Bioinformatics is integrative biology Your task is … To access available resources to maximise our understanding