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Following introduction to the various annotation tools, students can practice their newly acquired skills in the following exercises.
List of Annotation Exercises
Simple Annotation Problem
Last update: 12/23/2016
This worksheet will guide you through a series of basic steps that have been found to work well for annotation of species closely related to Drosophila melanogaster. It provides a technique that can also be the foundation of annotation in other, more divergent species but in those cases other special techniques will probably be needed.
Exercise #1: Detecting and Interpreting Genetic Homology
Last update: 12/13/2016
An introductory exercise using BLAST to annotate a region in the Drosophila melanogaster genome. Students can use this exercise to gain familiarity with performing BLAST searches and interpreting BLAST output. An answer key is provided for instructors.
Exercise #2: Using mRNA and EST Evidence in Annotation
Last update: 12/10/2016
This exercise allows students to learn how to use mRNA and Expressed Sequence Tags (ESTs) evidence to assist their annotation efforts. An answer key is available for instructors.
Browser-Based Annotation and RNA-Seq Data
Last update: 06/18/2011
This exercise continues your introduction to practical issues in comparative annotation. You will be annotating genomic sequence from the dot chromosome of Drosophila mojavensis using your knowledge of BLAST and some improved visualization tools. You will also consider how best to integrate information from high-throughput sequencing of expressed RNA.
Worksheet: Chimp BAC Analysis: Genes and Pseudogene
Last update: 12/08/2016
A step-by-step tutorial that takes the student through a gene identification problem in a chimpanzee BAC sequence using predictions from a gene finder (Genscan), the UCSC Browser and BLAST.
Guidelines for your Chimp Chunks Report
Last update: 02/19/2014
Brief guidelines with advice on annotating chimpanzee DNA, including what to put in the final report.
Analysis of a Chimp Chunk
Last update: 04/17/2006
Following the step-by-step tutorial, students should be ready to annotate a chunk of chimpanzee DNA themselves, presenting evidence to support their claim of a gene or pseudogene. An example student report from the Bio 4342 course at WU is available here.
Sample Chimp Chunk Reports
Last update: 02/01/2008
Three sample chimp chunk projects with student reports:
Chimp Chunk Projects without Student Reports
Last update: 02/01/2008
Additional chimp chunk projects without student reports. Please refer to the GEP wiki for instructions on how to create additional chimp annotation projects.