PPT-Gene Finding and Sequence Annotation

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. tracking, including browsing of an annotation's edit history and full undo/redo functions. Real. -time updating: edits in one client are instantly pushed to all other clients. Convenient . management of user login, authentication, and edit permissions. 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 . Marcus Chibucos, Ph.D.. University of Maryland School of Medicine. June 2014. Overview & goals. Understand. 1. How we predict . presence & structure . of coding & non-coding genes in the genome. Expanding Exposure, Career Exploration and Interactive Projects in Basic Genome Analysis and . Bioinformatics. Program Overview – National Science Foundation ITEST Strategies Project. Recruitment of 30 high school science teachers and 150 students per year to be involved in the annotation process (3 years total funding).. . AGeS: A Software System for Annotation and Analysis of Genome Sequences . *jaques.reifman@us.army.mil (301) 619-7915 . Kamal Kumar, Valmik Desai, Li Cheng, Maxim Khitrov, Deepak Grover, Ravi Vijaya Satya, Chenggang Yu, Nela Zavaljevski, and . Chris Shaffer July 2012. Last update: 08/2018. Annotation . “Big Picture” of annotation and then one practical example. This technique may not be the best with other projects (e.g. corn, bacteria). . approaches. Genomics Lesson . 7_2. Hardison. 3/1/15. 1. 3. approaches . to gene predictions. Evidence-based. Transcribed regions. Align to mRNA sequence from the same species. Align to spliced ESTs from the same species. BMI/CS 776 . www.biostat.wisc.edu/bmi776/. Spring . 2018. Anthony Gitter. gitter@biostat.wisc.edu. These slides, excluding third-party material, are licensed under . CC BY-NC 4.0. by Mark Craven, Colin Dewey, and Anthony Gitter. 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). BMI/CS 776 . www.biostat.wisc.edu/bmi776/. Spring 2020. Daifeng. Wang. daifeng.wang@wisc.edu. These slides, excluding third-party material, are licensed . under . CC BY-NC 4.0. by Mark . Craven, Colin Dewey, Anthony . Yanbin Yin. Fall 2014. 1. Outline. Intro to EBI. Databases and web tools. UniProt. Gene Ontology. Hands on Practice. MOST MATERIALS ARE FROM: http. ://www.ebi.ac.uk/training/online/course-. list. 2. Three international nucleotide sequence databases. HMM ‘fair-coin’ example. October 09. E. F. (H)=0.5. E. L. (H)=0.1. 0.6. 0.6. 0.4. 0.4. 1. H H T T T is the observed sequence. October 09. E. F. (H)=0.5. E. L. (H)=0.1. 0.6. 0.6. 0.4. 0.4. 0. 1. 0.6. 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.). 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?.