Melina protocols

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Melina specifications

Information


Unique identifier OMICS_09574
Name Melina
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 1.1
Stability Stable
Maintained Yes

Maintainer


  • person_outline Kenta Nakai <>

Additional information


Previous version: http://melina1.hgc.jp/

Publications for Melina

Melina in pipeline

2015
PMCID: 4686930
PMID: 26692124
DOI: 10.1038/srep18708

[…] for vertebrates, insects, and nematodes was used. a consensus sequence for the amplified regions of the tested promoters was also analysed using the consensus motif-finding algorithms consensus from melina ii and using default parameters amongst potential div and extrinsic promoters (camv 35s, cmv, and nos promoters)., how to cite this article: kadono, t. et al. characterization of marine […]


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Melina in publications

 (5)
PMCID: 5499772
PMID: 28158431
DOI: 10.1093/dnares/dsw065

[…] to detect the nf-y site as an erse., for comparison, the same gene list from the microarray data of tunicamycin response has been applied to gibbs sampler, meme, consensus and md scan provided by melina ii. these four methods could not detect either erse-a or erse-b (data not shown)., predictions using our bipartite octamers are shown in red letters in . both the bzip and nf-y binding sites […]

PMCID: 5105302
PMID: 27832791
DOI: 10.1186/s12934-016-0584-6

[…] the underlying sequences responsible for the expression levels and regulatory patterns observed in this study, we analyzed various groups of the characterized promoter sequences using the online melina ii program [], which provides analysis from four different motif finder programs (consensus, meme, gibbs, and mdscan). by analyzing all 25 synechococcus sp. pcc 7002 promoters cloned […]

PMCID: 4686930
PMID: 26692124
DOI: 10.1038/srep18708

[…] expression from div promoters, we attempted to find conserved motifs among the div promoter regions (cdp1, clp1, and clp2) using a consensus motif-finding algorithm (consensus) available through melina ii and using default parameters. the “ggcaggcg” sequence was detected in cdp1, clp1, and clp2 through the consensus algorithm. in the sense strand of clp1, there are three tandem repeats […]

PMCID: 3372377
PMID: 22518007
DOI: 10.1093/dnares/dss013

[…] confirmed by northern analysis (fig. ). figure 2. figure 3., next, we searched for conserved elements in the 5′ upstream and 3′ downstream regions of the genes in each group using the web-based tool melina ii (http://melina2.hgc.jp/public/index.html). no conserved elements were found in the 5′ upstream region; however, we identified a conserved element in the 3′ downstream region of genes […]

PMCID: 3058078
PMID: 21349196
DOI: 10.1186/1471-2229-11-39

[…] experiments. although there are several well-established methodologies for the prediction in motif-based search algorithms (gibbs sampler [,], meme [,], and their parallel analysis platform, melina ii []), we needed an octamer-based approach in order to give compatibility to reg analysis. in this report, we describe the development of an octamer-based prediction method using microarray […]


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Melina institution(s)
Mitsui Knowledge Industry Co. Ltd, Tokyo, Japan; RIKEN Genomic Sciences Center, Tokyo, Japan; Human Genome Center, Institute of Medical Science, University of Tokyo, Japan
Melina funding source(s)
Supported in part by Grant-in-Aid for Scientific Research on Priority Areas ‘Comprehensive Genomics’ from the Ministry of Education, Culture, Sports, Science and Technology of Japan.

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