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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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No version available

Documentation


Maintainer


  • person_outline Troels Marstrand

Publication for ASAP

ASAP citations

 (4)
library_books

Genome Wide Location Analysis Reveals Distinct Transcriptional Circuitry by Paralogous Regulators Foxa1 and Foxa2

2012
PLoS Genet
PMCID: 3380847
PMID: 22737085
DOI: 10.1371/journal.pgen.1002770

[…] ed 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 and […]

library_books

Isoform Diversity and Regulation in Peripheral and Central Neurons Revealed through RNA Seq

2012
PLoS One
PMCID: 3260295
PMID: 22272348
DOI: 10.1371/journal.pone.0030417

[…] ers of expressed isoforms mediated by cell-specific factors –. Thus we identified promoter regions for each isoform found to be overexpressed in one neuronal type compared to the other, and then used ASAP, an online tool, to estimate the relative abundance of TF binding sites (TFBSs) in these two groups of promoters (compared to a “background” set of randomly chosen promoters . Relative abundances […]

library_books

Transcriptional regulation of gene expression clusters in motor neurons following spinal cord injury

2010
BMC Genomics
PMCID: 2900267
PMID: 20534130
DOI: 10.1186/1471-2164-11-365

[…] ifferentially 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 […]

library_books

MicroRNA 145 Targets YES and STAT1 in Colon Cancer Cells

2010
PLoS One
PMCID: 2809101
PMID: 20098684
DOI: 10.1371/journal.pone.0008836

[…] position specific weight matrices (PSSMs) using a background nucleotide frequency of 25% and pseudocount of 1. The search for matches to these PSSMs in the promoter sequences were performed with the Asap software package using a threshold of 0.8. The percentage of promoters with hits for a given transcription binding site was compared between the down and the no-change sets or between the up and […]


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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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