PPT-The Integrated Microbial Genome (IMG) systems

Nikos Kyrpides Genome Biology Program GBP DOE Joint Genome institute IMG Genes Genomes Functions Metadata Clusters SNPs Proteomics Regulons Transcriptomes IMG Systems Data Types. The FortiGate Product Family: Integrated Multi-The FortiGate product family provides cost-effective, DATASHEET Copyright 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”. 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; . a. widely distributed . immunoregulatory. microbial . product. Matthew Rhodes and Catherine . Lozupone. University of Colorado, Denver. Rocky Mountain Bioinformatics Conference. December 11. th. 2014. Venter et. al (2004). Presented by. Ken . Vittayarukskul. Steven S. White.. Context of the Problem . Evolutionary history is directly tied to microbial genetics. Little is known. Until recently, microbial diversity was measured by PCR amplification and sequencing of only ribosomal genes. NEON’s 30-year sampling strategy for monitoring ecosystem productivity and biogeochemistry includes co-located measurements of plant structure, biomass, soil and plant biogeochemistry, and microbial populations. The resulting data can be used to address a wide variety of questions related to ecosystem science. This overview focuses on the measurements associated with two specific components of this design: soil biogeochemistry and microbial diversity (page 2), and plant structure and biogeochemistry (page 3). Scaling point measurements of these ecosystem components across space relies heavily on NEON’s Airborne Observation Platform (AOP), which will fly over all NEON sites annually to collect . Production Genomics Facility. “. User facility. providing high-throughput DNA sequencing & analysis in support of DOE missions in alternative . energy. , . carbon cycling . & . bioremediation. Bas E. Dutilh. March 4. th. 2013. Protein function. Phenotypic. . function. E.g. . apoptosis. GO: . Biological. . process. Cellular. . function. E.g. . ribosome. GO: . Cellular. component. Molecular. “. User facility. providing high-throughput DNA sequencing & analysis in support of DOE missions in alternative . energy. , . carbon cycling . & . bioremediation. .”. Opened in 1999. ~240 UC Employees. Loren Hauser. Miriam Land. Yun-Juan Chang. Frank Larimer. Doug Hyatt. Cynthia Jeffries. NEB Educational Support. 2. http://www.neb.com/nebecomm/course_support.asp?. Why study Computational Biology. . Hardison. Genomics5_1. 2/17/15. 1. Types of data in genomics. Protein and DNA sequences . Protein structure and function. Comparisons of DNA and protein sequences. Between species. Among individuals within a species. immunoregulatory. microbial . product. Matthew Rhodes and Catherine . Lozupone. University of Colorado, Denver. Rocky Mountain Bioinformatics Conference. December 11. th. 2014. Mazmanian. and Kasper . Figure 9.01. PCR Detection of . Sequence Tagged Site. Mapping large genomes requires many . genetic markers. . Those based solely on their unique sequences are known as sequence tagged sites (STS). These unique sequences may be amplified by PCR and mapped relative to each other. In practice, each STS is defined by a pair of specific PCR primers at its ends that generate a PCR fragment of defined length.. Nikos. . Kyrpides. DOE . Joint Genome institute. Two main goals of genome analysis:. Evolutionary analysis. How does an organism compare to the rest?. Metabolic reconstruction. What can an organism do and how?.