Import from Genbank workaround

[Peter Richterich]

Several users have reported problems using the "Import from Genbank" function in CodonCode Aligner. The import fails with an error message, for example "Invalid ID - Unknown format". This post describes the cause of the problem. Please note that this problem was fixed in CodonCode Aligner version 7.0.1.

Problem Cause
On November 9, 2016, Genbank has disabled all unencrypted access (through HTTP), allowing only access through HTTPS (announcement here). All CodonCode Aligner versions up to 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.

Workaround (functional only until October 1, 2017!)
Until October 1, 2017, the workaround described below worked. Instead of Genbank, data were downloaded from the EMBL-EBI web server. As of October 1, 2017, however, the EBI web server also used https access, so that the workaround described below fails!

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

Please note that this workaround fails as of October 1, 2017, since the EBI web server now also uses only secure (https) access. If you have followed the instructions above in the past, it is likely that the "Import from Genbank" function now fails, even in CodonCode Aligner version 7.0.1 and newer. If importing from Genbank fails, please remove the three lines shown above from the CodonCode Aligner Preferences file (note that all three lines must be removed, and that they may be at different locations in the preference file!).
Alternatively (for example if you prefer to use the EBI web server over the NCBI server), you can modify the "GenbankImportUrlStart" line to use https instead of http:

Code: Select all

GenbankImportUrlStart=https://www.ebi.ac.uk/ena/data/view/
GenbankImportIdPrefix=
GenbankImportIdPostfix=&display=text

Since now both the NCBI and the EBI web servers only support https access, and CodonCode Aligner version 6.0.2 and older do not support https access, users of older versions need to upgrade to version 7.0.1 or newer to use the "Import from Genbank" function.