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Chris Shaffer

GEP Hybrid Assembly Walkthrough

This document illustrates how students can apply the sequence improvement protocol described in the “Sequence Improvement Protocol for GEP Hybrid Assembly Projects” document to specific problems in a D. biarmipes sequence improvement project. Specifically, the walkthrough describes techniques for correcting consensus errors and for closing gaps.

UNIX for Consed

This PowerPoint presentation discusses the basic directory structure required by Consed and the UNIX commands used to launch Consed.

Gene Finding in Chimpanzee

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.

About Synteny Analysis

A one-page summary of the logic process used to determine if genes in a fosmid are syntenic with respect to D. melanogaster

Quick Check of Student Annotations

This document describes a protocol that GEP faculty can use to quickly identify potential errors in student gene annotations.

Basics of BLAST

This PowerPoint presentation provides a brief introduction to the different kind of BLAST searches available.

D. mojavensis: Issues of Polymorphisms

This PowerPoint presentation discusses the potential sequence improvement issues caused by single nucleotide and insert polymorphisms in the D. mojavensis and D. grimshawi projects.