Frequently asked Questions
Why are only a select few species included on the site?
In short: this is for speed. There is a database of precomputed features behind the system that allows things to run much faster. If you have a species you wish to consider, please contact us.
Why do I get different results if I use different interactions, sequences or parameters?
The method is sensitive to several things that vary if one varies things like interaction sets, total sequences, sequence filtering, or other parameters. This is particularly true as motifs themselves are very common, meaning that the difference between being seen (say) in 7 out of 9 sequences and being seen in 4 out of 5 sequences can be drastic. The only suggestion here is to be careful about which interactions or sequences you use to discover motifs, and to try multiple parameter sets. In practise, strong motifs tend to occur no matter what one does (short of filtering them all out of the input). A particularly potentially cryptic difference is when using amino acid grouping. Changes here lead to differences, for example, in the total number of species found among the instances of a motif, which then changes the orthology correction factors. This shouldn't make an enormous difference, but can account for why the same motif doesn't get exactly the same enrichment P-value.