Biological networks are rich representations of the relationships between entities such as genes or proteins and have become increasingly complete thanks to various high-throughput network mapping experimental approaches. Here, we propose a method to use such networks to guide the search for functional sequence motifs. Specifically, we introduce Local Enrichment of Sequence Motifs in biological...

The detection of motifs has recently become an important part of network analysis across all disciplines. In order to detect these network motifs, software such as FANMOD and MAVisto has been created. Although relatively quick in detecting small motifs, this software is comparatively slower when identifying large motifs, such as those of size six or seven. As a result of this time constraint, t...

In this paper, we consider the problem of finding all maximal motifs in an input string for the class of repeated motifs with wild cards. A maximal motif is such a representative motifs that is not properly contained in larger motifs with the same location lists. The enumeration problem for maximal motifs with wild cards has been introduced in (Parida et al., SODA’00, CPM’01), and has been stud...