wEMBOSS does not always handle all kinds of data in an optimal way. We mention here a few known bugs/misfeatures and how to get around them.

It can happen that, after login, the Project Management page or one of its frames is not displayed correctly and that instead you get an error message of the type:

You don't have permission to access /wEMBOSS_cgi/catch on this server.

You can easily fix this by clicking with the right button of the mouse to pop up a menu from which you can do a Refresh or Reload.

If you want to run fuzznuc, fuzzpro or fuzztran using a pattern that starts with '<' there is a problem. Depending on what flavour of UNIX/Linux is installed on the server, it can happen that wEMBOSS fails to pass the < correctly to the program. If this happens then you should not type the pattern into the Search pattern box but instead write it to a file in your project and then type @filename into the Search pattern box. Also, in the wEMBOSS program output page the '<' is interpreted as an HTML tag, causing the output to be truncated. This might disturb you, but you can always view the output correctly by clicking on right click to save locally.

For programs that need a codon usage table as part of their input, wEMBOSS displays a selector with all the .../share/EMBOSS/data/CODONS/*.cut files. If the CUTG databank has been installed on your server this selector gets more than 20000 entries and becomes unusable. There is currently no out-of-the-box solution. We will mention that in the EMBOSS installation of the Belgian EMBnet Node a hacked version of cutgextract stores the CUTG files with the extension .cutg rather than .cut, so that the file names do not appear in the selector (this allows users wishing to use a CUTG file to save it using embossdata, see above).

pepwindow and pepwindowall allow you to use, as an alternative data file, a file from the AAINDEX databank. There is no convenient way to access these data under wEMBOSS. If AAINDEX has been installed on your server you can save the file you need using embossdata (see above).