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

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 ma...

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Detalles Bibliográficos
Autores principales: Okumura, Toshiyuki, Makiguchi, Hiroki, Makita, Yuko, Yamashita, Riu, Nakai, Kenta
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933176/
https://www.ncbi.nlm.nih.gov/pubmed/17537821
http://dx.doi.org/10.1093/nar/gkm362
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author Okumura, Toshiyuki
Makiguchi, Hiroki
Makita, Yuko
Yamashita, Riu
Nakai, Kenta
author_facet Okumura, Toshiyuki
Makiguchi, Hiroki
Makita, Yuko
Yamashita, Riu
Nakai, Kenta
author_sort Okumura, Toshiyuki
collection PubMed
description 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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spelling pubmed-19331762007-07-31 Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions Okumura, Toshiyuki Makiguchi, Hiroki Makita, Yuko Yamashita, Riu Nakai, Kenta Nucleic Acids Res Articles 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. Oxford University Press 2007-07 2007-05-30 /pmc/articles/PMC1933176/ /pubmed/17537821 http://dx.doi.org/10.1093/nar/gkm362 Text en © 2007 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ 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.
spellingShingle Articles
Okumura, Toshiyuki
Makiguchi, Hiroki
Makita, Yuko
Yamashita, Riu
Nakai, Kenta
Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions
title Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions
title_full Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions
title_fullStr Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions
title_full_unstemmed Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions
title_short Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions
title_sort melina ii: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933176/
https://www.ncbi.nlm.nih.gov/pubmed/17537821
http://dx.doi.org/10.1093/nar/gkm362
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