PPT-Advancing Genome-Scale Phylogenomic Analysis

Tandy Warnow Departments of Computer Science and Bioengineering Carl R Woese Institute for Genomic Biology The University of Illinois at UrbanaChampaign httptandycsillinoisedu O r a. Denovo genome Denovo genome outline outline novogenome from contigs from assembled contigs annotation Denovo genome Denovo genome Reads contig Gene Gene Annotation Gene Annotation Forgene An International Human Rights Funders Group, Foundation Center, . Ariadne. : European Funders for Social Change and Human Rights , and International Network of Women’s Funds Initiative. What is IHRFG?. Mayo/UIUC Summer . C. ourse in Computational Biology. Session Outline. Genome sequencing. Schematic overview of genome assembly. (a) DNA is collected from the biological sample and sequenced. (b) The output from the sequencer consists of many billions of short, unordered DNA fragments from random positions in the genome. (c) The short fragments are compared with each other to discover how they overlap. (d) The overlap relationships are captured in a large assembly graph shown as nodes representing . BCB 660. October 20, 2011. From Carson Holt. Annotations. Automated. Ab. initio. (based on genomic sequence alone). Involves comparisons to known proteins (BLAST similarity). Sequence motifs such as start/stop . Raw Scale Raw Scale Raw Scale Raw Scale Score Score Score Score Score Score Score Score 86 100 64 80 42 66 20 42 85 98 63 79 41 66 19 41 84 97 62 79 40 65 18 39 83 95 61 78 39 64 17 38 82 94 60 77 38 Basic Biology: DNA. Genetic information is stored in . deoxyribonucleic acid (DNA) . molecules.. A single DNA molecule is a sequence of . nucleotides. adenine (. A. ). cytosine (. C. ). guanine (. G. Mayo/UIUC Summer . C. ourse in Computational Biology. Session Outline. Genome sequencing. Schematic overview of genome assembly. (a) DNA is collected from the biological sample and sequenced. (b) The output from the sequencer consists of many billions of short, unordered DNA fragments from random positions in the genome. (c) The short fragments are compared with each other to discover how they overlap. (d) The overlap relationships are captured in a large assembly graph shown as nodes representing . Lecture 1: Introduction. Linkage studies. Traditional approach to identifying genes for human traits and diseases was through linkage.. For . Mendelian. diseases (e.g. Huntington’s disease) there is a clear co-segregation of genetic markers with disease within pedigrees.. Nadia Khan, Rick Smith, . and Anna . Kuperman. Epigenetics 2012. Introduction. Most Genome Wide Approaches were adapted from technologies originally developed for detecting methylation at the level of a single gene. Scale, Scale Factor, & Scale Drawings. Objective:. 7.2.01 & 7.3.03. Essential Question:. . How can I use a scale factor to understand distances on a map or the size of a house or object?. Vocabulary:. Isabella. Roland. Sarahi. Veronica. General protocol. Isolation of . vibrios. . DNA extraction. Illumina. sequencing. Assembly and annotation. Quality of data.  . Year . HS0A . 2012. HS0B . 2012. HS0C . Genomics and Society Nature (2014) “ …disorders not readily explained by standard tests can sometimes be diagnosed through genome sequencing and analysis.” The Origin of “Genomics& Benjamin Neale, PhD. Boulder Workshop. Content warning: eugenicists. Sick individuals and sick populations Rose 1985. Mendelian. Genetics. Co-dominance. East 1915: Inheritance of Corolla Length in . http://ncgas.org. . Carrie . Ganote. Ram . Podicheti. Le-Shin Wu. Tom . Doak. Quality Control and Assessment of. RNA-. Seq. Data. National Center for Genome Analysis Support: . http://ncgas.org. .