Using the SSH connection you can send Fasta and BLAST searches to be run on the remote machine. If you have not already be prompted to login (i.e. when opening up the SSH file manager), you will then be asked for your login details. The sequence files that are to be searched against the database are then sent to the remote machine. Once the search has finished the results are transferred back afterwards. If Artemis detects that you have opened up an entry from the remote file system the analysis will be run in the directory you open the entry from. The results in this case are stored on both the local and remote machines.
To keep Fasta and BLAST searches on your local machine and the remote file system in-sync:
copy any previously run fasta and blast directories from the remote machine to your local file system. This can be done by making a tar ball of the directory: e.g. creating a tar file of a 'fasta' directory
tar cvf tar_ball_name.tar fasta
Then transfer this file to the local project directory and extract with:
tar xvf tar_ball_name.tar
when launching Artemis, make sure you first change directory to the directory above the 'fasta' directory that has been unpacked.
open the files from the remote file system in the file manager. It then knows where to save it back to.