PPT-Genome mapping

Genome sequencing Next Gen sequencing Genomics resources genome maps genome sequences genome clones DNA microarrays whole gene collections functional genomics 1980 1998 1977 2003 DNA mapping. 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 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. Genome Browser. Combines a genome database with interactive web pages. Allows the user to retrieve and manipulate database record through a graphical user interface (GUI). Different types of information are displayed in an intuitive fashion in user-configurable “tracks”. Shai. Carmi. Pe’er. lab, Columbia University. and. The Ashkenazi Genome Consortium (TAGC). Boston. September 2013. Outline. Ashkenazi Jewish (AJ) Genetics . and TAGC. Basic Variant Statistics. Utility in AJ Medical . From Swab to Publication. Madison I. Dunitz. 1. , David A. Coil. 1. , Jenna M. Lang. 1. , Guillaume Jospin. 1. , Aaron E. Darling. 2. , Jonathan A. Eisen. 1. UC Davis Genome Center. 1. University of California, Davis; . 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 . By Kevin Chen, . Lior. . Pachter. PLoS. Computational Biology, 2005. David Kelley. State of . metagenomics. In July 2005, 9 projects had been completed.. General challenges were becoming apparent. Paper focuses on computational problems. Computations . to GPUs. Graphics processors (GPUs) and other . “wide SIMD” multiprocessors . are becoming . a dominant force in high-performance computing.. How do we effectively use them for . streaming applications . 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. . Egusquiza. D145 Presentation. January 12, 2017. What is genome mapping?. http://www.yourgenome.org/facts/how-do-you-map-a-genome. The use of various methods to determine the locus of a genetic landmarks (genes, regulatory sites, etc.) and the relative distances between genetic landmarks in the genome. Dan Gilchrist. National Human Genome Research Institute. October 18, 2016. The ENCODE Project. 3D Data Access Through the ENCODE Portal. The ENCODE Encyclopedia. Tools for Investigating Genetic Variants. 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 . . Egusquiza. D145 Presentation. January 12, 2017. What is genome mapping?. http://www.yourgenome.org/facts/how-do-you-map-a-genome. The use of various methods to determine the locus of a genetic landmarks (genes, regulatory sites, etc.) and the relative distances between genetic landmarks in the genome.