MELINA: motif extraction from promoter regions of potentially co-regulated genes

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MELINA: motif extraction from promoter regions of potentially co-regulated genes

UNLABELLED 'Melina' assists users to compare the results of four public softwares for DNA motif extraction in order to both confirm the reliability of each finding and avoid missing important motifs. It is also useful to optimize the sensitivity of software with a series of different parameter settings. AVAILABILITY Melina is available at http://www.hgc.ims.u-tokyo.ac.jp/Melina/.

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“Melina” - Novel Tool for Elucidation of Consensus Motif in the Promoter Regions of Functionally Related DNA Sequences

Gene expression is controlled by protein factors that interact with DNA promoter regions to affect transcription. To understand the regulation of gene expression means knowing about the transcription factors and the DNA sites at which they act. Microarray analysis of gene expression profile are considered to be the most systematic experimental approach at present, which allows to identify and a...

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Promoter Analysis of Co-regulated Genes in the Yeast Genome

The use of high density DNA arrays to monitor gene expression at a genome-wide scale constitutes a fundamental advance in biology. In particular, the expression pattern of all genes in Saccharomyces cerevisiae can be interrogated using microarray analysis where cDNAs are hybridized to an array of more than 6000 genes in the yeast genome. In an effort to build a comprehensive Yeast Promoter Data...

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Combining phylogenetic motif discovery and motif clustering to predict co-regulated genes

MOTIVATION We present a sequence-based framework and algorithm PHYLOCLUS for predicting co-regulated genes. In our approach, de novo discovery methods are used to find motifs conserved by evolution and then a Bayesian hierarchical clustering model is used to cluster these motifs, thereby grouping together genes that are putatively co-regulated. Our clustering procedure allows both the number of...

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MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes

Understanding the complex mechanisms regulating gene expression at the transcriptional and post-transcriptional levels is one of the greatest challenges of the post-genomic era. The MoD (MOtif Discovery) Tools web server comprises a set of tools for the discovery of novel conserved sequence and structure motifs in nucleotide sequences, motifs that in turn are good candidates for regulatory acti...

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ژورنال

عنوان ژورنال: Bioinformatics

سال: 2003

ISSN: 1367-4803,1460-2059

DOI: 10.1093/bioinformatics/btf872