tailieunhanh - Báo cáo sinh học: "SMOTIF: efficient structured pattern and profile motif search"

Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí y học Molecular Biology cung cấp cho các bạn kiến thức về ngành sinh học đề tài: SMOTIF: efficient structured pattern and profile motif search. | Algorithms for Molecular Biology BioMed Central Research Open Access SMOTIF efficient structured pattern and profile motif search Yongqiang Zhang and Mohammed J Zaki Address Department of Computer Science Rensselaer Polytechnic Institute Troy New York 12180 USA Email Yongqiang Zhang - zhangy0@ Mohammed J Zaki - zaki@ Corresponding author Published 21 November 2006 Received 21 May 2006 Algorithms for Molecular Biology 2006 1 22 doi 1748-7188-1 -22 Accepted 21 November 2006 This article is available from http content 1 1 22 2006 Zhang and Zaki licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License http licenses by which permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited. Abstract Background A structured motif allows variable length gaps between several components where each component is a simple motif which allows either no gaps or only fixed length gaps. The motif can either be represented as a pattern or a profile also called positional weight matrix . We propose an efficient algorithm called SMOTIF to solve the structured motif search problem . given one or more sequences and a structured motif SMOTIF searches the sequences for all occurrences of the motif. Potential applications include searching for long terminal repeat LTR retrotransposons and composite regulatory binding sites in DNA sequences. Results SMOTIF can search for both pattern and profile motifs and it is efficient in terms of both time and space it outperforms SMARTFINDER a state-of-the-art algorithm for structured motif search. Experimental results show that SMOTIF is about 7 times faster and consumes 100 times less memory than SMARTFINDER. It can effectively search for LTR retrotransposons and is well suited to searching for motifs with long range gaps. It is also successful in finding .