PMC:1679804 / 134831-135638 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1679804","sourcedb":"PMC","sourceid":"1679804","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1679804","text":"We have implemented the SMOTIF algorithm in standard C++. We compare our results with SMARTFINDER, the best previous algorithm for structured motif search. For fair comparison, the suffix tree used in SMOTIF-2 for finding the pos-list of simple motifs is the same as the one used in SMARTFINDER, namely the lazy mode suffix tree [11], and we apply Sellers' dynamic programming algorithm [26] for approximate matching. The programs were compiled with g++ v3.2.2 at the optimization level 3 (-O3). Unless indicated otherwise, we did the experiments on an Apple G5 with dual 2.7Ghz processors and 4GB memory running Mac OS X; the timings reported are total times for all steps of the algorithms; all our experiments use exact matching for the simple motifs, and we report the full position for the occurrences.","tracks":[]}