Import from Genbank workaround

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Import from Genbank workaround

Postby Peter Richterich » Thu Nov 10, 2016 10:48 am

Several users have reported problems using the "Import from Genbank" function in CodonCode Aligner. The import fails with an error message "Invalid ID - Unknown format". This post describes the cause of the problem, and a workaround.

Problem Cause
On November 9, 2016, Genbank has disabled all unencrypted access (through HTTP), allowing only access through HTTPS (announcement here). All CodonCode Aligner version 6.0.2 try to access Genbank through HTTP, which now fails. Unfortunately, access to Genbank through HTTPS in older versions of CodonCode Aligner is not possible due to limitations in the Java versions used. We plan to fix this problem in future versions of CodonCode Aligner.

Workaround
To download sequences from nucleotide databases, CodonCode Aligner can be instructed to use the EMBL-EBI web server instead of Genbank. This can be done by adding three lines to the CodonCode Aligner settings file, as follows:
  1. Quit CodonCode Aligner if it is running
  2. Open a Finder or Explorer window and navigate to the folder where the CodonCode Aligner preference file is located.
    • On Mac OS X, this is the folder "CodonCode Aligner Preferences" in "Library/Preferences" in your home directory. Note that the Library folder may be hidden by OS X. One way to navigate there is to choose "Go to folder" from the "Go" menu in the Finder, and enter "~/Library/Preferences/CodonCode Aligner Preferences" (without the quotes)
    • On Windows, this is the folder "Aligner Preference Data" in "AppData\Roaming\CodonCode Aligner" in your home folder. The "AppData" folder may be hidden by the operating system, and you may need to use the Control Panel "Show hidden files and folders".
  3. Open the file "Aligner Preference Data" in a text editor like NotePad or TextEdit
  4. Add the following 3 lines to the file:
    Code: Select all
    GenbankImportUrlStart=http://www.ebi.ac.uk/ena/data/view/
    GenbankImportIdPrefix=
    GenbankImportIdPostfix=&display=text
  5. Save the file
You should need to do this only once on each computer and user account where you use CodonCode Aligner (unless you forgot to quit CodonCode Aligner first, since CodonCode Aligner will re-write the preferences file when it quits).
If you have problems locating the preferences file, you can check the "Aligner_errorlog.txt" file in the "Logs" folder where CodonCode Aligner is installed. At the beginning of each session entry, CodonCode Aligner lists the location of the settings file.
Peter Richterich
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