PPT-Functional Annotation of Formerly “

Unculturable SAR11 Bacteria Jim Tripp JGI Stanford Research Institute March 4 2013 Overview SAR11 biomass equals that of fish SAR11 cultured poorly in natural seawater only Genome revealed major surprises. Archaea. Matthew Blow. mjblow@lbl.gov. Adam . Deutschbauer. Morgan Price. Kelly Wetmore. Adam . Arkin. Cindi. Hoover. Feng. Chen. Jim Bristow. Deutschbauer. lab, LBNL. JGI. G. ene function annotation . 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 . &. Text Coding. Learning Target. I can determine a central idea of a text and how it is conveyed through particular details; provide a summary of the text distinct from personal opinions or judgments. . Abstract. A large number of organizations today generate and share textual descriptions of their products, services, and actions. Such collections of textual data contain significant amount of structured information, which remains buried in the unstructured text. While information extraction algorithms facilitate the extraction of structured relations, they are often expensive and inaccurate, especially when operating on top of text that does not contain any instances of the targeted structured information. . GO editors agreed on C16 relations . QuickGO graph of relations much less flat. 32. 51. Progress on Annotation extension relations. David OS transferred all . C16 relations . Wiki pages to . GitHub. and created new pages. A Close Reading Strategy for Better Comprehension. Text Annotation by Teachers. What is Text Annotation?. While reading, students mark the pages for . Important information. Text meaning or key details. Authors: Joe Futrelle, Amber York. . @ Woods Hole Oceanographic Institution. Imaging FlowCytobot. (Heidi Sosik et al). HabCam. (Scott . Gallager. et al). SeaBED. (. Hanumat. Singh et al). Phytoplankton . ConceptRank. Petra Budíková, Michal Batko, Pavel Zezula. Outline. Search-based annotation. Motivation. Problem formalization. Challenges. ConceptRank. Idea. Semantic network construction. PageRank and ConceptRank. Text Annotation by Teachers. What is Text Annotation?. While reading, students mark the pages for . Important information. Text meaning or key details. Ideas and questions. What About Highlighters?. The Next Generation. Rashmi. Prasad, Bonnie . W. ebber, . A. lan Lee. *. Aravind. Joshi. Outline. Introduction. Discourse Coherence and its annotation. PDTB Basics. PDTB enrichment. Motivation. New relations. (ideas for . joint journal paper). CEMI meeting, Praha, 14. 3. 2014. Outline. Introduction. Why annotations?. State-of-the-art in multimedia annotation. Search-based image annotation. What. . we. . Lecture 3. Gene Finding and Sequence Annotation. Objectives of this lecture. Introduce you to basic concepts and approaches of gene finding. Show you differences between gene prediction for prokaryotic and eukaryotic genomes. However, genomes are large and complex and visualizing this information is not easy. You need to imagine that the raw annotation information, by itself, can be contained in a text file, which could include positional information (coordinates relative to the reference genome) and different features (e.g. annotation type – gene, mRNA, intron/exon, variant, UTR, etc.). Program for today:. - . Functional. . annotation. . of. genes/. gene. . products. : Gene . Ontology. (GO). - . significance. . of. . annotations. : . hypergeometric. . test. - (. mathematical.