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Tools and Algorithms in Bioinformatics GCBA815, Fall 2015 Week9: Genome Analysis Tools (UCSC Browser, Galaxy) Guest demonstrator: Sanjit Pandey Babu Guda Department of Genetics, Cell Biology and Anatomy University of Nebraska Medical Center __________________________________________________________________________________________________ 10/30/2015 GCBA815 Terminology • Genome • Typically the nuclear genome in eukaryotes or the only genome in prokaryotes • Extra-nuclear genome • Mitochondrial and chloroplast genomes • Metagenome • A mixture of genomes belonging to multiple species that are not fully characterized • Epigenome • The characteristics of the genome that effects gene expression, such as chromatin packing, methylation, etc. • Pangenome • The union of the gene sets of all the strains of a species, typically applied to prokaryotes • Human Microbiome (microbe metagenome) • The set of all microbial genomes that harbor human body __________________________________________________________________________________________________ 10/30/2015 GCBA815 Genome sizes of species in the evolutionary spectrum __________________________________________________________________________________________________ 10/30/2015 GCBA815 Human Karyotype __________________________________________________________________________________________________ 10/30/2015 GCBA815 Statistics on Human Genome • Haploid nuclear genome size (3.0 x 109 ) • Female-3,227 Mbp; Male-3,122 Mbp • Chromosomes: 1-22, X, Y, all linear • Highly conserved regions • Coding DNA covers about 50 Mbp (~1.5%) • Other regulatory regions cover about 100 Mbp (3%) • Repetitive DNA covers more than 50% • Segmental duplication: more than 5% • Endogenous retroviral genomes (ERVs): 5-8% (inherited) • Other associated genomes • Mitochondrial genome: about 16.5 Kbp, circular genome • Viral genomes (transfected exogenous Retroviruses) • Microbiome (over 2000 different microbial flora harbor human body) __________________________________________________________________________________________________ 10/30/2015 GCBA815 Statistics on Human Exome • Exome includes the protein coding region and the flanking untranslated regions (5’ UTR and 3’ UTR) • Exome studies usually include the protein coding regions covering about 30 Mbp of DNA (~1%) • Human genome has approximately 180,000 exons • An estimated 85% of the disease causing mutations exist on exons; hence, clinical sequencing heavily targets exome sequencing • On average there are 9 exons per gene, but the number varies by gene length, which ranges from 1-363. • The Titin gene (TTN) has 363 exons. • Average exon length is about 122 bp • Exons with 3’ UTRs are considerably longer __________________________________________________________________________________________________ 10/30/2015 GCBA815 Statistics on Human Genes/Proteins • About 25K genes code for about 100,000 proteins in human • Not all expressed at the same time or at the same location • Mitochondrial genes: 37 (code for 22 tRNAs, 13 proteins and 2 rRNAs) • Retroviral proteins • About 3.5 million genes encoded by about 2000 microbiome flora • Oral microbiome, gut microbiome, etc. • Known genes: ~21,667 (source Ensembl) • Novel genes: 1,013 • Pseudogenes: 1,040 __________________________________________________________________________________________________ 10/30/2015 GCBA815 UCSC Genome Browser http://genome.ucsc.edu • Portal for many reference genomes, ENCODE and Neanderthal projects • Genome Browser Other Tools • Gene Sorter: Displays a sorted list of related genes • Genome Graphs: Tool to display genome-wide datasets and results of association studies • BLAT: Quick mapping of sequences to genome • Table Browser: Provides access to the underlying database • VisiGene: To browse the in situ collection of the mouse and frog images __________________________________________________________________________________________________ 10/30/2015 GCBA815