Finding motifs in the twilight zone

We introduce the notion of a multiprofile and use it for finding subtle motifs in DNA sequences. Multiprofiles generalize the notion of a profile and allow one to detect subtle consensus sequences that escape detection by the standard profiles. Our MULTIPROFILER algorithm outperforms other leading motif finding algorithms in a number of synthetic models. Moreover, it can be shown that in some previously studied motif models, MULTIPROFILER is capable of pushing the performance envelope to its theoretical limits.

• Type: Conference
• Year: 2002
• Where: RECOMB
• Authors: Uri Keich, Pavel A. Pevzner
• Keywords: Computational Biology, Motif Finding Algorithms, RECOMB 2002, Standard Profiles, Subtle Consensus Sequences