CodonCode Aligner Forum

In June 2024, users have reported that BLAST searches from CodonCode Aligner fail. This problem is caused by a change in the internet address parameters that the NCBI BLAST server expects. The problem can be fixed by adding a corrected entry for the BLAST server address (URL) in the CodonCode Aligner preferences file. The easiest and safest way to do this is by dragging and dropping a file with the required entry onto a CodonCode Aligner project window, following these steps:

• Download the blast_url.zip ZIP archive from https://www.codoncode.com/aligner/downl ... st_url.zip
• Locate the downloaded ZIP archive, and unpack it (extract the file "blast_url.alpref").
• Start CodonCode Aligner, and create a new project or open an existing project.
• Drag the "blast_url.alpref" file from step 2 onto the CodonCode Aligner project window (or use "Open" to open the "blast_url.alpref" file). This will update the CodonCode Aligner preferences to include the updates BLAST address.
• Try one of the BLAST options (from the "Go" menu) to verify that BLAST now works as expected.
• Quit CodonCode Aligner (so that the changes to the preferences are saved).

Instead of the method described above, expert users can also manually edit the CodonCode Aligner preferences file and add a line with the following content: This requires the use of a plain text editor, and that CodonCode Aligner is not running when making the changes. The location of the CodonCode Aligner preferences file is shown in the Aligner log file, which is in the "Logs" folder in the directory where CodonCode Aligner is installed. Manually editing the preferences file is generally not recommended - please use the file method outline above instead, if at all possible.