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New motif search algorithms and evaluation measures are developed based on these questions.
The motif search algorithms are based on Gusfield's Z-boxes (Gusfield, 1997).
It is notoriously difficult to choose representative negative sequence sets for evaluating motif search algorithms.
One data category involves the potential target genes of bZIP TFs, which are computationally predicted using phylogenetic footprinting and motif search algorithms [ 19, 20].
Exhaustive motif search algorithms have been proposed which rely on proper heuristics and pruning of the search space, such as the approach pioneered by Marsan and Sagot [ Marsan and Sagot, 2000].
Second, using de novo motif search algorithms (WebMotifs; http://fraenkel.mit.edu/webmotifs/ and [ 31]), we found that the promoters of these genes are highly enriched for the presence of the middle sporulation element (MSE) (specificity score 10-29), the known binding site of Ndt80 [ 11], [ 18].
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YH implemented and validated the motif search algorithm.
The motif search algorithm shall be able to find motifs containing variable regions.
Our motif search algorithm is different from previous attempts to find modules [ 19].
They propose a motif search algorithm which helps to describe the aptamers enrichment in more detail.
All these factors need to be considered when designing an efficient structured motif search algorithm.
Related(15)
motif searching algorithms
motif search options
motif inference algorithms
motif extraction algorithms
motif discovery algorithms
motif search results
motif recognition algorithms
motif detection algorithms
motif search profiles
motif identification algorithms
motif scanning algorithms
motif finding algorithms
motif search webservices
purpose search algorithms
pattern search algorithms
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