PPT-1 MICROBIAL GENOME ANNOTATION

Loren Hauser Miriam Land YunJuan Chang Frank Larimer Doug Hyatt Cynthia Jeffries NEB Educational Support 2 httpwwwnebcomnebecommcoursesupportasp Why study Computational Biology . 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”. 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 . PropBank. . Outline. Introduction to the project. Basic linguistic concepts. Verb & Argument. Making information explicit. Null arguments. Tasks to be carried out. Timesheets, tips. Creation of Resources. Massimo Poesio. University of . Essex. Part 1: Intro, . Microtask. . crowdsourcing. ANNOTATED CORPORA: . AN ERA OF PLENTY?. With the release of the . OntoNotes. and ANC corpora for English and a number of corpora for other languages (Prague Dependency Treebank especially) we may think we won’t need to do any more annotation for a while . &. 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. . 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. Philip . McParlane. , Yashar Moshfeghi and Joemon M. Jose. University of Glasgow, UK. http://www.dcs.gla.ac.uk/~philip/. p.mcparlane.1@research.gla.ac.uk. Motivation for annotating images. Problems with existing automatic image annotation collections. 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. 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. Daniel Standage. Biology Department. Indiana University. An-no-ta-. tion. . \ˌa. -. nə. -ˈ. tā-. shən. \. A critical or explanatory note or body of notes added to a text. The act of annotating. Last Updated: 12/26/2021. Wilson Leung and Chris Shaffer. Agenda. Overview of the GEP annotation project. GEP annotation strategy. Types of evidence. Analysis tools. Web databases. Annotation of a single isoform (walkthrough). 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.