PPT-Genome generation

Timetable for today Time Activity 0000 Introduction to the session 0010 Story cards 0020 Info cards 0030 Issue cards 0040 Discuss two key issues 0045 Feedback your issues What is DNA. sequencing . for . identification,. detection, . and control of . Bactrocera dorsalis (. Hendel. ). and other Tephritid pests. Thomas Walk, Scott . Geib. USDA-ARS Pacific Basin Agricultural Research Center, Hilo HI. 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 . 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”. 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 . 2. Some genomics history. 1995: first bacterial genome, . Haemophilus influenza. , 1.8 Mbp, sequenced at TIGR. first use of whole-genome shotgun for a bacterium. Fleischmann et al. 1995 became most-cited paper of the year (>3000 citations). 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. Active Roles in Evolution of . Immunity and Pregnancy . Retroviruses 2015. Chicago, June 8, 2015. James A. Shapiro. University of . Chicago. jsha@uchicago.edu. www.shapiro.bsd.uchicago.edu. . Evolutionary time: Genome writing . 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. Elaine R. . Mardis. – 11 . February. . 2008. Washington School of Medicine, Genome Sequencing Center.. Presented by . Jacob . Juhn. “If one accepts that the fundamental pursuit of genetics is to determine the genotypes that explain phenotypes, the meteoric increase of DNA sequence information applied toward that pursuit has nowhere to go but up.”. . John Glass. for members of the . Venter Institute Synthetic Genomics Group. The J. Craig Venter Institute, . Rockville, MD and San Diego, CA. Construction of a Bacterial Cell Containing Only Essential Genes Necessary to Impart . 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. Uploading Your Job. Login to your RAST account. You will need to register if this is your first time using SEED technologies to work with your genome.. Click on the “Upload a new job” link.. Click here!. Nikos. . Kyrpides. Genome . Biology . Program (GBP). DOE Joint Genome institute. IMG. Genes. Genomes. Functions. Metadata. Clusters. SNPs. Proteomics. Regulons. Transcriptomes. IMG Systems Data Types. 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.