Hello there. I am having some issues with the query designer in uGene. I have created a query schema, and when I try to use it, it says "No Matches Found". However, I know that matches should indeed be found. Basically, I am using multiple Smith waterman searches, in order to annotate a list of binding sites within the sequence. I notice that when I only use a couple of these Smith watermans, then the query works, but when I try to do it with around 15, I get that error message. Could you offer any advice? Thank you very much in advance for your assistance.

Jordan,

The bug may be caused by the Smith-Waterman's "Filter results" option. When it's set to "filter intersections" the Smith-Waterman algorithm may exclude an appropriate result (see the bug for details).

Could you please try to set the "Filter results" parameter of the Smith-Waterman elements to "None" and search again. If it does not help, we would like to get additional info so we could reproduce your problem. The ".uql" file and the sequence would help a lot.