TY - JOUR
T1 - Melina II
T2 - A web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions
AU - Okumura, Toshiyuki
AU - Makiguchi, Hiroki
AU - Makita, Yuko
AU - Yamashita, Riu
AU - Nakai, Kenta
N1 - Funding Information:
that made the following algorithms freely available: Consensus, Gibbs sampler, MEME, MDscan, Weeder, RefSeq, JASPAR, HMMER and Sequence Logo/WebLogo. We thank Nicolas Sierro also for critically reading the manuscript. This work was partly supported by Grant-in-Aid for Scientific Research on Priority Areas ‘Comprehensive Genomics’ from the Ministry of Education, Culture, Sports, Science and Technology of Japan. Funding to pay the Open Access publication charges for this article was provided
PY - 2007/7
Y1 - 2007/7
N2 - 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.
AB - 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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U2 - 10.1093/nar/gkm362
DO - 10.1093/nar/gkm362
M3 - Article
C2 - 17537821
AN - SCOPUS:34547555385
SN - 0305-1048
VL - 35
SP - W227-W231
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - SUPPL.2
ER -