PMC:1679804 / 159045-160162 JSONTXT

{"project":"2_test","denotations":[{"id":"17118189-8697238-1688086","span":{"begin":593,"end":594},"obj":"8697238"},{"id":"17118189-14980017-1688086","span":{"begin":593,"end":594},"obj":"14980017"},{"id":"17118189-11108467-1688087","span":{"begin":677,"end":679},"obj":"11108467"},{"id":"17118189-17109757-1688088","span":{"begin":995,"end":997},"obj":"17109757"}],"text":"Conclusion\nWe introduced SMOTIF, a fast and efficient algorithm to search structured pattern and profile motifs in biological sequences. We showed its applications in searching for composite regulatory patterns, long terminal repeat retrotransposons, and for searching long range motifs. SMOTIF is also computationally more efficient than previous state-of-the-art methods like SMARTFINDER [6].\nIn biosequence analysis there are four related structured motif problems depending on whether the simple motifs and gap ranges in the structured motif are known or not: (i) Structured motif search [4-6]: all simple motifs and gap ranges are known; (ii) Structured motif extraction [30-32]: all simple motifs are unknown and all gap ranges are known; (iii) Extended structured motif search: all simple motifs are known and all gap ranges are unknown; and (iv) Extended structured motif extraction: all simple motifs and gap ranges are unknown. In this paper we tackled problem (i). A companion paper [33] tackles problem (ii). In the future, we plan to develop efficient algorithms for the other two motif problems as well."}