Bellora, Nicolás, Farré, Domènec, Mar Albà, M PEAKS: identification of regulatory motifs by their position in DNA sequences. (Article) Bioinformatics (Oxford, England), 23 (2), pp. 243–4, 2007, ISSN: 1367-4811. (Abstract | Links | BibTeX | Tags: Algorithms, Automated, Automated: methods, Base Sequence, Chromosome Mapping, Chromosome Mapping: methods, DNA, DNA: genetics, DNA: methods, Molecular Sequence Data, Nucleic Acid, Nucleic Acid: genetics, Pattern Recognition, Regulatory Sequences, Sequence Alignment, Sequence Alignment: methods, Sequence Analysis, Software, Transcriptional Activation, Transcriptional Activation: genetics) @article{Bellora2007a,
title = {PEAKS: identification of regulatory motifs by their position in DNA sequences.},
author = {Bellora, Nicolás and Farré, Domènec and Mar Albà, M},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17098773},
issn = {1367-4811},
year = {2007},
date = {2007-01-01},
journal = {Bioinformatics (Oxford, England)},
volume = {23},
number = {2},
pages = {243--4},
abstract = {Many DNA functional motifs tend to accumulate or cluster at specific gene locations. These locations can be detected, in a group of gene sequences, as high frequency 'peaks' with respect to a reference position, such as the transcription start site (TSS). We have developed a web tool for the identification of regions containing significant motif peaks. We show, by using different yeast gene datasets, that peak regions are strongly enriched in experimentally-validated motifs and contain potentially important novel motifs. AVAILABILITY: http://genomics.imim.es/peaks},
keywords = {Algorithms, Automated, Automated: methods, Base Sequence, Chromosome Mapping, Chromosome Mapping: methods, DNA, DNA: genetics, DNA: methods, Molecular Sequence Data, Nucleic Acid, Nucleic Acid: genetics, Pattern Recognition, Regulatory Sequences, Sequence Alignment, Sequence Alignment: methods, Sequence Analysis, Software, Transcriptional Activation, Transcriptional Activation: genetics}
}
Many DNA functional motifs tend to accumulate or cluster at specific gene locations. These locations can be detected, in a group of gene sequences, as high frequency 'peaks' with respect to a reference position, such as the transcription start site (TSS). We have developed a web tool for the identification of regions containing significant motif peaks. We show, by using different yeast gene datasets, that peak regions are strongly enriched in experimentally-validated motifs and contain potentially important novel motifs. AVAILABILITY: http://genomics.imim.es/peaks |
Messeguer, Xavier, Escudero, Ruth, Farré, Domènec, Núñez, Oscar, Martínez, Javier, Albà, M Mar PROMO: detection of known transcription regulatory elements using species-tailored searches. (Article) Bioinformatics (Oxford, England), 18 (2), pp. 333–4, 2002, ISSN: 1367-4803. (Abstract | Links | BibTeX | Tags: Animals, Binding Sites, Binding Sites: genetics, Computational Biology, DNA, DNA: genetics, DNA: metabolism, Humans, Software, Species Specificity, Transcription Factors, Transcription Factors: metabolism) @article{Messeguer2002,
title = {PROMO: detection of known transcription regulatory elements using species-tailored searches.},
author = {Messeguer, Xavier and Escudero, Ruth and Farré, Domènec and Núñez, Oscar and Martínez, Javier and Albà, M Mar},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11847087},
issn = {1367-4803},
year = {2002},
date = {2002-01-01},
journal = {Bioinformatics (Oxford, England)},
volume = {18},
number = {2},
pages = {333--4},
abstract = {We have developed a set of tools to construct positional weight matrices from known transcription factor binding sites in a species or taxon-specific manner, and to search for matches in DNA sequences.},
keywords = {Animals, Binding Sites, Binding Sites: genetics, Computational Biology, DNA, DNA: genetics, DNA: metabolism, Humans, Software, Species Specificity, Transcription Factors, Transcription Factors: metabolism}
}
We have developed a set of tools to construct positional weight matrices from known transcription factor binding sites in a species or taxon-specific manner, and to search for matches in DNA sequences. |
