POXO protocols

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POXO specifications

Information


Unique identifier OMICS_24751
Name POXO
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained No

Maintainer


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Publication for POXO

POXO in pipelines

 (2)
2017
PMCID: 5733009
PMID: 29312363
DOI: 10.3389/fpls.2017.02049

[…] corresponding to motif length of 6–8 nt, 8–10 nt, and 10–12 nt, respectively. the statistically-significant motifs were screened for similarity with known transcription factor binding motifs using poxo (kankainen et al., ) (http://ekhidna.biocenter.helsinki.fi/poxo) and stamp (mahony and benos, )., promoters of nrrs genes identified along with the previously reported genes as positive control […]

2008
PMCID: 2613404
PMID: 19036124
DOI: 10.1186/1471-2199-9-105

[…] additional file . these patterns were then aligned with clustalw [], (additional file )., the most significant motifs were located from the putative mirna regulatory region with visualize tool of poxo tool series [], or weeder motif locator included in mod tools [], allowing two mismatches to the consensus sequence, and the position weight matrices were calculated from these results. […]


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POXO in publications

 (3)
PMCID: 5733009
PMID: 29312363
DOI: 10.3389/fpls.2017.02049

[…] the promoter region of all 51 genes to identify nrrs motif (supplementary figure presentation ; supplementary figure ). to identify the transcription factors that might bind to these sites, we used poxo (kankainen et al., ) and stamp (mahony and benos, ) but no statistically significant similarity to known motifs was found. therefore, further characterization of these novel motifs is required […]

PMCID: 3123201
PMID: 21595952
DOI: 10.1186/1752-0509-5-77

[…] tair-atgenexpress (http://www.ebi.ac.uk/microarray-as/ae/), geo (ncbi) (http://www.ncbi.nlm.nih.gov/geo/) []., (see attached file for experiment descriptions)., a number of tools in the poxo (http://ekhidna.biocenter.helsinki.fi/poxo) [] promoter analysis suite were used to analyze promoter regions 2000 bp upstream of the coding regions of the genes in the psy-ecg50. the poco tool […]

PMCID: 2613404
PMID: 19036124
DOI: 10.1186/1471-2199-9-105

[…] additional file . these patterns were then aligned with clustalw [], (additional file )., the most significant motifs were located from the putative mirna regulatory region with visualize tool of poxo tool series [], or weeder motif locator included in mod tools [], allowing two mismatches to the consensus sequence, and the position weight matrices were calculated from these results. […]


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POXO institution(s)
Institute of Biotechnology and University of Kuopio, Kuopio, Finland; Department of Biological and Environmental Sciences, Genetics, University of Helsinki, Helsinki, Finland; Laboratory of Functional Genomics and Bioinformatics, Department of Neurobiology, A.I. Virtanen Institute for Molecular Sciences, Kuopio, Finland; Department of Biochemistry and Department of Computer Science, University of Kuopio, Kuopio, Finland
POXO funding source(s)
Supported by the Academy of Finland (grant no. 1105182), by a grant from the Ministry of Education, and by the Finnish Cultural Foundation.

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