title: Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions.
abstract: 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.
authors.affiliation: Mitsui Knowledge Industry Co. Ltd, University of Tokyo, Japan.
authors.forename: Toshiyuki
authors.initials: T
authors.lastname: Okumura
authors.forename: Hiroki
authors.initials: H
authors.lastname: Makiguchi
authors.forename: Yuko
authors.initials: Y
authors.lastname: Makita
authors.forename: Riu
authors.initials: R
authors.lastname: Yamashita
authors.forename: Kenta
authors.initials: K
authors.lastname: Nakai
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D003628:Database Management Systems; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D011401:Promoter Regions, Genetic; D011506:Proteins / Q000737:chemistry; D011786:Quality Control; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D011506:Proteins