POCO protocols

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POCO specifications

Information


Unique identifier OMICS_24743
Name POCO
Alternative name POCO 2nd
Interface Web user interface
Restrictions to use None
Database management system MySQL
Computer skills Basic
Stability Stable
Maintained No

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Information


Unique identifier OMICS_24743
Name POCO
Alternative name POCO 2nd
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output data A file containing F-score sorted patterns that are assigned into five groups by comparing the results of the HSD-tests.
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained No

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Publication for POCO

POCO in pipeline

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

[…] was set to 10. even though the initial width of the sites was entered as 8, the output sites had length of 8 or more, where 8 columns were conserved and the rest of them were non-conserved., from poco results for both worms, we chose such patterns that were found from every sequence in the putative mirna regulatory sequence sets, having p-values less than 0.05 and searched among […]


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POCO in publications

 (4)
PMCID: 5684745
PMID: 29158724
DOI: 10.1186/s12953-017-0128-y

[…] of the m. oryzae version 8 genome were assigned by the wolf psort program []. the 500 bp upstream of open reading frames were searched for hgatar domains (h = a, c or t and r = a or g) using the poco motif finding program [] and the presence of hgatar motifs were compared between gene of interests and background genes., in this study, the protein profiles of m. oryzae 70–15 mycelia grown […]

PMCID: 4148386
PMID: 25109818
DOI: 10.3892/mmr.2014.2465

[…] were retrieved from the ucsc genome database (http://genome.ucsc.edu/). the sequence patterns over-represented or under-represented in these two promoter sequence sets were analyzed by the poco program (http://ekhidna.biocenter.helsinki.fi/poxo/poco/poco). poco identifies motifs that are over-represented in one dataset compared with a background set, but under-represented in another […]

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

[…] mirnas (25 of these were located within a protein coding gene) and 95 caenorhabditis briggsae mirnas, were searched for conserved over-represented sequence patterns with four motif finding tools: poco, weeder, meme and gibbs motif sampler., with poco, 65 significant patterns that occur in every sequence in both c. elegans and c. briggsae putative mirna promoter sequence sets were found (table […]

PMCID: 1929144
PMID: 17504544
DOI: 10.1186/gb-2007-8-5-r83

[…] some results, but they turned out to be of limited use. these results are given in tables s3 and s4 (in additional data file 5), respectively. creme [] did not find any module. the output of poco [], consisting of five lists of short sequences representing overrepresented tfbss, is not directly comparable with the output of our approach because our approach takes into account […]


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POCO institution(s)
Institute of Biotechnology, University of Helsinki, Helsinki, Finland; Department of Biosciences, Division of Genetics, University of Helsinki, Helsinki, Finland
POCO funding source(s)
Supported by a grant from the Ministry of Education.

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