2008 Washington University ongoing projects

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The page is designed to list all projects currently under development for the use by the GEP prior to eventual release to the main GEP web site. 

Finishing Lab Practice using Drosophila virilis

  • Title: Finishing Lab Practice using Drosophila virilis
  • Author(s): Andrew Nylander & Chris Shaffer
  • Brief Description: These are a "simple" and "complex" walk-through designed to cover the basics of using Consed and solving finishing problems using two different projects from Drosophila virilis. As a walk-through, it is designed for students to follow along at their computers, as they are taken through various steps in finishing. This starts with an easy project (green clone, editing only) and then moves on to a more difficult project (reassembly and gap closing required). It does not pose questions that students could answer to create a graded worksheet.
  • Current Status: Completed, Posted the the GEP web page under curriculum - course materials - Sequence improvement
  • Contact: Chris Shaffer

Drosophila Finishing Homework/Worksheet

  • Title: Drosophila Finishing Homework/Worksheet
  • Author(s): Andrew Nylander & Chris Shaffer
  • Brief Description: The goal is a worksheet that can be done either in class or as homework that deals with various topics in finishing using Drosophila virilis projects. This worksheet should create a replacement for the Mouse worksheet but deal more directly problems students may encounter when finishing Drosophila species.
  • Current Status: Under active development.
  • Contact: Chris Shaffer

Update to Annotation HW2

  • Title: Homework 2
  • Author(s): Wilson Leung
  • Brief Description: Updated HW2 which uses online tools to assist students in the incorporation of EST evidence in manual annotation of a section of chimanzee.
  • Current Status: Completed, Posted the the GEP web page under curriculum - course materials - Annotation 
  • Contact: Wilson Leung

Annotation Instruction Sheet

  • Title: Annotation Instruction Sheet
  • Author(s): Chris Shaffer
  • Brief Description: This is a more in depth description/consideration of the evidence based annotation technique used by the GEP. This document is designed to complement and extend the basic technique described in the Annotation of D. virilis powerpoint [[2]], this powerpoint has also been updated to better complement the instruction sheet. The instruction sheet includes more advice on how to resolve ambiguous annotation issues and attempts to help define relative importance of various forms of evidence.
  • Current Status: Completed, now available on the main GEP web site.
  • Contact: Chris Shaffer

Annotation Worksheet

  • Title: Annotation Worksheet
  • Author(s): Andrew Nylander & Chris Shaffer
  • Brief Description: The goal is to create a worksheet which walks students through various annotation problems in D. virilis; this would be a substitute for chimp chunks. It would ask questions which can be used in class discussion or answered by students as part of a graded problem set. This will mostly cover the topics covered in the Annotation Instruction Sheet.
  • Current Status: In preparation, just started
  • Contact: Chris Shaffer

Annotation: Double Checking Your Gene Models

  • Title: How to double check your models
  • Author(s): Chris Shaffer
  • Brief Description: This will be a simple write up of what to do after you have completed your gene model. The paper will include both the use of the gene checker (which will check for compliance with known basic biology) and how to double check the model based on the underlying analysis that was done. The basic protocol here is to do a final blast2seq alignment between your new gene model and the putative Drosophila melanogaster ortholog. The results of this alignment should be interpreted based on the annotation work done on this gene to double check that this pairwise alignment recapitulates the annotation work (i.e. do the regions that were found to be conserved align as expected and are the regions that do not show alignment correlate with the regions where no conservation was found). As a second double check use the Gene Checker to generate a GFF file that can be used to create custom track on the GEP version of the UCSC browser for your fosmid. The custom track can be compared back to the data found in the browser to provide an additional check on the gene model. Ideally the students will be able to read and follow along with their own data and by the end will have found any underlying problems or will have more confidence that they have the best possible model.
  • Contact: Chris Shaffer