PPT-Genome 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 startstop . 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 Tao Huang, . Shrideep. . Pallickara. , Geoffrey Fox. Community Grids Lab. Indiana University, Bloomington. . {. taohuang. , . spallick. , . gcf}@indiana.edu. Outline. Analysis of existing Collaboration and Annotation Systems. Triplets to Sentence Fingerprints. Motivation. . Scientific concepts are annotated with controlled vocabulary (CV) terms from ontologies such as Gene Ontology (GO) and Plant Ontology (PO). . Our Arabidopsis specific tool - . 2. n-gram language model. 3. classifier. Studying Humour Features - Bolla, Whelan. Guidelines. define tags and describe how they should be applied. Data. 500 reviews of varying length (>7300 sentences). 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. Loralee Chevone-Garrett and Beth Dibble. ANNOTATION IS NOT. A coloring assignment. A detailed analysis. Exact or correct. Busy work. Teacher-centered. WHAT IS ANNOTATION?. RESEARCH SAYS.... A writing-to-learn strategy for use while reading and rereading.. 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. 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. 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 . 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.).