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Nucleic Acids Research Advance Access first published online on May 30, 2007
This version published online on May 31, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm362
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions

Toshiyuki Okumura1, Hiroki Makiguchi1, Yuko Makita2, Riu Yamashita3 and Kenta Nakai3,*

1Mitsui Knowledge Industry Co. Ltd, 2RIKEN Genomic Sciences Center and 3Human Genome Center, Institute of Medical Science, University of Tokyo, Japan

*To whom correspondence should be addressed: Tel: +81-3-5449-5131; Fax: +81-3-5449-5133; Email: knakai{at}ims.u-tokyo.ac.jp

Received January 30, 2007. Revised April 13, 2007. Accepted April 25, 2007.

We present the second version of Melina, a web-based tool for promoter analysis. Melina II shows potential DNA motifs in promoter regions with a combination of several available programs, Consensus, MEME, Gibbs sampler, MDscan and Weeder, as well as several parameter settings. It allows running a maximum of four programs simultaneously, and comparing their results with graphical representations. In addition, users can build a weight matrix from a predicted motif and apply it to upstream sequences of several typical genomes (human, mouse, S. cerevisiae, E. coli, B. subtilis or A. thaliana) or to public motif databases (JASPAR or DBTBS) in order to find similar motifs. Melina II is a client/server system developed by using Adobe (Macromedia) Flash and is accessible over the web at http://melina.hgc.jp.


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