Resource Image

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)

3 comment(s) (Post a comment)

Summary:
In this activity, students are introduced to dotplots as a tool for analyzing phage genomic similarity.

Licensed under CC Attribution-ShareAlike 4.0 International according to these terms

Version 1.0 - published on 24 Aug 2020 doi:10.25334/RR9F-HD75 - cite this

Alignments

    Comments

    1. 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.  :( 

      Copy link Report abuse

      Your reply
      No attachment

      Your edits
      No attachment

      1. 0 Like

        Christa Bancroft @ on

        Hugely helpful, thank you!  I couldn't figure out why it would open, yet not find any files.  

        Copy link Report abuse

        Your reply
        No attachment

        Your edits
        No attachment

      2. 0 Like

        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 

         

        Copy link Report abuse

        Your reply
        No attachment

        Your edits
        No attachment