Title :
Identification of structured motifs
Author :
Sheng, Huitao ; Mehrotra, Kishan ; Mohan, Chilukuri ; Raina, Ramesh
Author_Institution :
Dept. of Electr. Eng.&Comput. Sci., Syracuse Univ., Syracuse, NY, USA
Abstract :
Structured motifs consist of two simpler patterns (half-sites) separated from each other by a gap, with no restriction on the nucleotides that may occur within the gap. This paper proposes a new algorithm to identify structured motifs. First, a simpler motif searching algorithm is used to search for half-sites. Candidate structured motif models are then evaluated, based on the relative frequency of occurrence of half-sites (not attributable to randomness), and the distribution of gap length. Unlike other recent structured motif detection algorithms, the new algorithm does not require the gap length to be prespecified.
Keywords :
biology computing; cellular biophysics; genetics; gap length; half-sites; motif searching algorithm; nucleotides; structured motifs; Algorithm design and analysis; Biology; Computer science; DNA; Detection algorithms; Frequency; Gene expression; Organisms; Random sequences; Stress;
Conference_Titel :
Bioinformatics and Biomedicine Workshop, 2009. BIBMW 2009. IEEE International Conference on
Conference_Location :
Washington, DC
Print_ISBN :
978-1-4244-5121-0
DOI :
10.1109/BIBMW.2009.5332103