FAQ

Q: Why are the nodes different colours after a run?

Once a run is completed, nodes which have SLiMs will change to red diamonds to indicate this; the darker shade of red means that there is more than one SLiM in the node.

Q: I did a run, but I only got one node in the graph produced. What went wrong?

When a run is completed, the graph produced doesn't have a layout so all the nodes are stacked on top of one another. Going to the "Layout" tab and selecting a layout will change the configuration of the graph nodes (and make them appear).

Q: My runs are returning an error, but I know that there are SLiMs present. What's going on?

There are several possible reasons for this:

1. If your nodes are in the same domain or if there are too few of them, there is insufficient data for the server to work with. Try adding some more nodes and see if that fixes the problem.
2. If you're running SLiMProb, then perhaps the specific SLiM you're looking for is not present, even though others are. Try running SLiMFinder and see what results appear there.

Q: My SLiMProb motif consistently causes errors/doesn't seem to work.

Most often, this is because the motif doesn't obey our regex rules (even though it may obey the regex rules for other services). Our regex rules for inputting a motif are as follows:

• A = single fixed amino acid.
• [AB] = A or B. Any number of options may be given, e.g. [ABC] = A or B or C.
• <R:m:n> = At least m of a stretch of n residues must match R, where R is one of the above regular expression elements.
• [^A] = not A.
• X or . = Wildcard positions (any amino acid). Can be followed by {m,n} = At least m and up to n wildcards.
• R{n} = n repetitions of R, where R is any of the above regular expression elements.
• ^ = Beginning of sequence
• $ = End of sequence
• (R|S)= match R or S, which are both themselves recognisable regular expressions.