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

Toshiyuki Okumura, Hiroki Makiguchi, Yuko Makita, Riu Yamashita, Kenta Nakai

Research output: Contribution to journalArticlepeer-review

31 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)W227-W231
JournalNucleic acids research
Volume35
Issue numberSUPPL.2
DOIs
Publication statusPublished - 2007 Jul

ASJC Scopus subject areas

  • Genetics

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