PPT-The Out-of-Place Testing for Genome Comparison

HsinHsiung Huang PhD Assistant Professor Department of Statistics University of Central Florida 1 1162015 B ackgrounds An ngram used in text mining or linguistics is equivalent to a k. 1 CD6 SE Fig 1 CD XT SE Fig 1 CD8 SE Fig 1 CD ransport brPage 3br 325 1015 Reading 325 325 Fig 3 17 59 57 Fig 2 1 1 1 brPage 4br Cyrus CD 6 SE 2 CD 8 SE 2 CD XT SE 2 CD T TRANSPORT User Instructions 1 IMPORTANT Read before operating this equipme 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 Jeroen. . Raes. , Jan O . Korbel. , Martin J . Lercher. , Christian von . Mering. and Peer Bork. Presented by Daehwan Kim. Outline. Genome size. Genome sizes of Archaea, Bacteria, and Eukaryotes. Factors affecting genome and genome sizes . The Plot. Deepak . Purushotham. Hamid Reza . Hassanzadeh. Haozheng. . Tian. Juliette . Zerick. Lavanya. . Rishishwar. Piyush. . Ranjan. Lu Wang. The Outline. The Need & The Requirement. The Options. (as told by Michael Lynch). Genome size and complexity varies across the tree of life. Lynch 2007. Some Big Questions. What is the relationship between genomic and organismal size/complexity?. Are genome size changes adaptive, or passively acquired?. from Biological . Problem to . Combinatorial Algorithms. (and back). Pavel Pevzner. Department of Computer . Science,. . University . of California at San Diego. What is the evolutionary scenario for transforming one genome into the other?. 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. CUT THIS OUT CUT THIS OUT CUT THIS OUT CUT THIS OUT CUT THIS OUT CUT THIS OUT CUT THIS OUT CUT THIS OUT CUT THIS OUT CUT THIS OUT CUT THIS OUT CUT THIS OUT CUT THIS Birth Place Married Place Death Place Birth Place Death Place Birth Death Birth Place Married Place Death Place Birth Place Married Place Death Place Birth Place Death Place Birth Birth Birth Place De Fyodor D. Urnov, PhD. Project Leader and Senior Scientist, Sangamo BioSciences, Inc.. NAS International . Summit on Human Gene . Editing. December 3, 2015. Genome Editing . Is. In the Clinic. Fyodor D. Urnov, PhD. Genome: the total number of genes in an individual.. Human Genome- approx. 20,000 genes on the 46 human chromosomes.. Human Genome Project (HGP). Ongoing effort to completely map and sequence our genome.. 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 . G-OnRamp Beta Users Workshop. Wilson Leung. 07/2016. Outline. Obtain genome assemblies from NCBI. Transfer . large genomics datasets to Galaxy. Common bioinformatics file formats . D. atatypes in Galaxy. Wylie KM, Wylie TN, Orvedahl A, Buller RS, Herter BN, Magrini V, et al. Genome Sequence of Enterovirus D68 from St. Louis, Missouri, USA. Emerg Infect Dis. 2015;21(1):184-186. https://doi.org/10.3201/eid2101.141605.