ASAP protocols

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ASAP specifications

Information


Unique identifier OMICS_16679
Name ASAP
Interface Web user interface
Restrictions to use None
Programming languages R
License GNU General Public License version 3.0
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Troels Marstrand <>

Information


Unique identifier OMICS_16679
Name ASAP
Software type Framework/Library
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Source code URL http://asap.binf.ku.dk/c_source/
Maintained Yes

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Documentation


Maintainer


  • person_outline Troels Marstrand <>

Publication for ASAP

ASAP in pipeline

2011
PMCID: 3068983
PMID: 21410980
DOI: 10.1186/1471-2164-12-152

[…] strands of each human region defined above with position weight matrices (pwms) (reviewed in []) from the jaspar database (models ma0065.2 and ma0019.1, respectively, for pparγ and c/ebpα) using the asap tool [] based on a background model following a uniform distribution. to decide a relevant threshold for accepting a predicted binding site, we repeated the analysis in randomly selected regions […]


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ASAP in publications

 (3)
PMCID: 3380847
PMID: 22737085
DOI: 10.1371/journal.pgen.1002770

[…] for de novo motif finding. sequence alignment of foxa proteins was performed by clustalw2 algorithm . analysis of overrepresented functional categories was carried out as described previously ., the asap software was used for positional weight matrix enrichment analysis (parameters: fisher's exact test, sequence-based statistics, pwm threshold 0.8) , scoring the matrices from jaspar database […]

PMCID: 2900267
PMID: 20534130
DOI: 10.1186/1471-2164-11-365

[…] expressed genes using biomart. each set of promoter sequences pertaining to a distinct time profile was analyzed for over- and under-represented transcription factor binding sites using asap [] with position weight matrices (pwm) obtained from jaspar [] or transfac []. asap searches the set of promoter sequences using a transcription factor motif (i.e. pwm) and calculates the number […]

PMCID: 2848542
PMID: 20369014
DOI: 10.1371/journal.pcbi.1000729

[…] were used as the negative (background) set. known motifs were identified by using position frequency matrices of all known motifs stored in the transfac database . the motif enrichment analysis tool asap was used to scan all transfac motif matrices against the positive sequence sets of each reporter metabolite. the negative sequence sets were used together with 2nd order background model. […]


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ASAP institution(s)
Bioinformatics Centre, Department of Molecular Biology and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark; Swiss Institute of Bioinformatics, Swiss Institute for Experimental Cancer Research (ISREC), Epalinges, Switzerland
ASAP funding source(s)
Supported by a grant from the Novo Nordisk Foundation and by the SNSF grant PBLAA-109445.

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