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Posted by doi 10. 1093nargkm362. PMCID PMC1933176Copyright The AuthorsMelina II web tool for comparisons among several predictive algorithms to find potential motifs from promoter regionsToshiyuki Okumura,1 Hiroki Makiguchi,1 Yuko Makita,2 Riu Yamashita,3 and Kenta Nakai31Mitsui Knowledge Industry Co. Sequence logos new way to display consensus sequences. Nucleic Acids Res. 6. Stormo, GD Hartzell, GW. Nat.
Sequence logos new way to display consensus sequences. 4. Kel, A KelMargoulis, O Borlack, J Tchekmenev, D Wingender, Genome Res. To support this function, we previously released web tool named Melina 5. Recently, it was updated to its second version, Melina II. Each DNA sequence was randomly generated by the Random Sequence Generator, which is function of Melina II. Detected motif candidates are illustrated with colored arrows in the summarized view upperright corner of the result view. thaliana or to public motif databases JASPAR or DBTBS in order to find similar motifs. 200634D95D97. Science.
This article has been cited by other articles in PMC. AbstractWe present the second version of Melina, webbased tool for promoter analysis. Extraction of common TFBS from set of DNA sequences is practically important problem. 19898611831187. Nucleic Acids Res.
Recently, it was updated to its second version, Melina II. The integration of algorithms based on different principles should help detecting subtle motifs and reducing the number of false positives. 6. Stormo, GD Hartzell, GW. Bailey, Douglas In Melina II, some of the integrated algorithms are replaced with more modern ones and the graphical representation is extensively improved. Vol. Funding to pay the Open Access publication charges for this article was provided by budget from the Ministry of Education, Culture, Sports, Science and Technology of Japan. Users can later access the results by using this job ID.
Bailey, Douglas Handbook of Toxicogenomics. Thus, to avoid missing important motifs relying on only one algorithm or to check the effect of changing parameter values, it is useful to compare the prediction results obtained from different algorithmsparameter values. Melina II shows potential DNA motifs in promoter regions with combination of several available programs, Consensus, MEME, Gibbs sampler, MDscan and Weeder, as well as several parameter settings. 14.
We thank Nicolas Sierro also for critically reading the manuscript. 253290. 5. Poluliakh, N Takagi, T Nakai, The integration of algorithms based on different principles should help detecting subtle motifs and reducing the number of false positives. Phone 81354495131, Fax 81354495133, Email knakaiatims. utokyo. ac. jp Received 30, 2007 Revised 13, 2007 Accepted 25, 2007. This is an Open Access article distributed under the terms of the Creative Commons Attribution NonCommercial License which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Published online 20041411881190. Motifs were set in random order to check the influence of their location.
Tags: algorithms, amp, science and technology