Using Dotplots for Comparative Genomic Analysis
Author(s): Andrew Kapinos1, Canela Torres1, Amanda Freise1, Sean McClory2, Kathleen Cornely3
1. UCLA 2. La Salle University 3. Providence College
1083 total view(s), 940 download(s)
Summary:
In this activity, students are introduced to dotplots as a tool for analyzing phage genomic similarity.
Contents:
- Annotating dotplots constructed using Gepard.pptx(PPTX | 9 MB)
- Dotplot Learning Activity Outline.docx(DOCX | 40 KB)
- Dotplot_Learning Activity Instructions.docx(DOCX | 2 MB)
- Dotplot_Part A_Pre-activity.docx(DOCX | 997 KB)
- Dotplot_Part A_Pre-activity_Answer Key.docx(DOCX | 1015 KB)
- Dotplot_Part B_Post-activity assessment.docx(DOCX | 18 KB)
- Using Gepard to make dotplots.pptx(PPTX | 4 MB)
- License terms
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Johann Peter Gogarten @ on (Edited: @ on )
The latest version of macOS X has some incompatibilities with JAVA. After checking a few help pages I found that openjava works nicely.
To install openjava, I first deleted the Oracle version:
I went to /Library/Java/JavaVirtualMachines and deleted both folders which were there.
Then I went to https://adoptopenjdk.net/archive.html? and downloaded and installed jdk-11.0.9+11.1 (both JRE and jdk)
Using the command-line in the terminal application the java version then was reported as follows:
> java -version
openjdk version "11.0.9" 2020-10-20
OpenJDK Runtime Environment AdoptOpenJDK (build 11.0.9+11)
OpenJDK 64-Bit Server VM AdoptOpenJDK (build 11.0.9+11, mixed mode)
To start Gepard I used the command-line via the terminal application (Gepard-1.40.jar was placed in the /Applications folder):
> java -jar /Applications/Gepard-1.40.jar
Starting the program through double-clicking started the program, but did not give access to the program to access files. :(
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Christa Bancroft @ on
Hugely helpful, thank you! I couldn't figure out why it would open, yet not find any files.
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Johann Peter Gogarten @ on (Edited: @ on )
Update: The 2.1 version of Gepard under Mac OS 12.1 can be started through double clicking :)
In the new version of MacOSX, you need to give disk access to the program to load files from directories in your home folder. Go to system settings (under the apple pulldown menu on the top left), select privacy and security, select full disk access.
Click on the + at the bottom and then navigate to the "java" program. On my computer this was at
/Library/Java/JavaVirtualMachines/adoptopenjdk-11.jdk/Contents/Home/bin/java
You need to do the same for the Javalauncher (click on the + again)
on my system this is at
/System/Library/CoreServices/JavaLauncher.app
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