Annotation Unix Worksheet
Exercise that uses UNIX tools (command-line BLAST and RepeatMasker) for gene annotations.
Exercise that uses UNIX tools (command-line BLAST and RepeatMasker) for gene annotations.
A simple exercise on using simple Unix commands to navigate to different directories and manipulate files.
A Unix reference sheet for commonly used Unix commands.
PowerPoint presentation with instructions for running BLAST, RepeatMasker, and the BLAST output viewer Herne on the command-line.
Students can practice using Consed by working on a mouse contig. This exercise poses various challenges that students may encounter when working on their own projects.
This PowerPoint presentation explains our strategy, detailing the source of the raw sequence data for the D. grimshawi dot chromosome.
This document describes the list of tools developed by the GEP to facilitate incorporation of additional reads from the NCBI Trace Archive into a sequence improvement project. This document shows how to install the tools, and illustrates their use in two case studies (walkthroughs) of challenging fosmid assemblies.
Students should complete all items on this checklist before submitting the project back to the GEP.
This document contains advice on the strategies students can use to resolve common problems they may encounter during sequence improvement.
Students will typically need to request additional sequencing reactions in order to improve the quality of an assembly. This document describes some of the key considerations that students should keep in mind when they design oligonucleotide primers.