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Recent motif finding development provides user-friendliness via Web interface.
From the observations above, we see that the future of the motif finding development for ChIP-Seq should be Web tool design with user-friendly interface.
We also observed that recent motif finding development tends to exploit the Web for providing ease of use to the users.
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Finally, we provided our suggestions for future development of motif finding Web tool that better assists researchers for finding motifs in ChIP-Seq data.
Many de novo motif finding tools have been developed to detect these unknown motifs.
Many tools have been developed for motif finding.
In [22], they find that the motif finding effort is greatly enhanced by referencing to nearby gene structure and identifying "peak regions" where motifs can be isolated.
To identify potential cis-regulatory elements involved in splicing regulation for development, we applied de novo motif finding algorithms MEME [ 61] and BioProspector [ 62].
Since PSO is designed to work in multidimensional continuous domains, this paper presents required developments to adapt PSO for the motif finding application.
Many motif finding algorithms, for example references [4] [15], have been developed and the performance of motif finding algorithms has been steadily improving.
We observed that newer motif finding Web tools have the capability to find global over-represented motifs, local over-represented motifs, and alternative motifs.
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