A motif extraction algorithm based on hashing and modulo-4 arithmetic.
We develop an algorithm to identify cis-elements in promoter regions of coregulated genes. This algorithm searches for subsequences of desired length whose frequency of occurrence is relatively high, while accounting for slightly perturbed variants using hash table and modulo arithmetic. Motifs are evaluated using profile matrices and higher-order Markov background model. Simulation results show that our algorithm discovers more motifs present in the test sequences, when compared with two well-known motif-discovery tools (MDScan and AlignACE). The algorithm produces very promising results on real data set; the output of the algorithm contained many known motifs.
Sheng
Huitao
H
Department of Electrical Engineering and Computer Science, Syracuse University, Syracuse, NY 13244, USA. hsheng@syr.edu
Mehrotra
Kishan
K
Mohan
Chilukuri
C
Raina
Ramesh
R
D000465:Algorithms; D001483:Base Sequence; D005786:Gene Expression Regulation; D023281:Genomics; D011401:Promoter Regions, Genetic; D050436:Regulatory Elements, Transcriptional; D017422:Sequence Analysis, DNA