1. Specify the input sequences
All the input sequences must be in one-letter amino acid
code. The allowed alphabet (not case sensitive) is as follows:
A C D E F G H I K L M N P Q R S T V W Y
Please note that the sequences containing other symbols e.g. X
(unknown) will be discarded before processing. The sequences can be input
in the following two ways:
Paste a single sequence (just the amino acids) or a number of sequences in
format into the upper window of the main server page.
Select a FASTA
file on your local disk, either by typing the file name into the lower window
or by browsing the disk.
Both ways can be employed at the same time: all the specified sequences will
be processed. However, there may be not more than 10 sequences
in toto in one submission.
The sequences shorter than 15 or longer than 4000 amino
acids will be ignored.
2. Select the output format
By default the server only shows the final predictions. If you unclick the
button labelled "Show predictions only" the progress of the prediction
process will be reported in detail.
3. Submit the job
Click on the "Submit" button. The status of your job (either 'queued'
or 'running') will be displayed and constantly updated until it terminates and
the server output appears in the browser window.
At any time during the wait you may enter your e-mail address and simply leave
the window. Your job will continue; you will be notified by e-mail when it has
terminated. The e-mail message will contain the URL under which the results are
stored; they will remain on the server for 24 hours for you to collect them.
ArchaeaFun is dependent on a number of other programs that have to be run on
the input sequences prior to employing the ArchaeaFun method itself. Therefore,
the processing of multiple sequences may be time-consuming. In the case of
prolonged wait the user is advised to use the e-mail option mentioned