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TRAP specifications

Information


Unique identifier OMICS_08382
Name TRAP
Alternative name Transcription factor Affinity Prediction
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input data A single DNA sequence.
Operating system Unix/Linux
Programming languages C++, R
Computer skills Advanced
Version 3.04.01
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Morgane Thomas-Chollier <>

Additional information


http://trap.molgen.mpg.de/cgi-bin/help.cgi

Information


Unique identifier OMICS_08382
Name TRAP
Alternative name Transcription factor Affinity Prediction
Interface Web user interface
Restrictions to use None
Input data Some DNA sequences.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Morgane Thomas-Chollier <>

Additional information


http://trap.molgen.mpg.de/cgi-bin/help.cgi

Publications for Transcription factor Affinity Prediction

TRAP in pipeline

2017
PMCID: 5343793
PMID: 28134766
DOI: 10.3390/ijms18020257

[…] using snp annotation and proxy search (snap) with an r2 threshold of 0.8 and a distance limit of 500 kb []. ld was calculated with the northern europeans from utah (ceu) population. we also used the transcription factor affinity prediction (trap) web tools for single sequences to measure the possible transcription factor binding affinities to tagged snp regions in the presence or absence of snps […]

TRAP in publications

 (16)
PMCID: 5800657
PMID: 29408916
DOI: 10.1371/journal.pone.0192385

[…] the 3’-utr and to predict if a snp within the target site will disrupt/eliminate or enhance/create a microrna binding site. perfectos-ape (http://opera.autosome.ru/perfectosape/scan) and s-transcription factor affinity prediction (s-trap, http://trap.molgen.mpg.de/cgi-bin/trap_two_seq_form.cgi) were used to identify transcription factors whose binding sites can be significantly […]

PMCID: 5888794
PMID: 29385519
DOI: 10.1093/nar/gky051

[…] were counted per fragment to obtain interaction profiles. for more details, see ., to identify ctcf binding motif-matches at ctcf-chip peaks (figure and ), we analyzed regions of interest using the transcription factor affinity prediction (trap) webtool (). for more details, see ., to study the global connection between gr binding and gr-dependent gene regulation, we combined data […]

PMCID: 5815073
PMID: 29309647
DOI: 10.1093/nar/gkx1242

[…] -g hg19 -m -bg bg/k562/hela.transfac.bg) (). resulting motifs were converted into pwms as described above and utilized for further analysis via stap tools.trap graphical representationstrap v3.05 (transcription factor affinity prediction) generated the graphical output for stap analysis and displays the predictions of relative binding affinities for tfbitr and non-tfbitr regions ()., […]

PMCID: 5748627
PMID: 29113108
DOI: 10.3390/jpm7040015

[…] (ceu) population []. the r2 was 80% and the distance limit was 500 kb. gwas catalog was then used to verify if tagged and non-tagged snps have been previously identified in a gwas []. finally, the transcription factor affinity prediction (trap) web tool for two sequences was used to evaluate transcription factor binding affinity differences between the alleles of tagged snps [,,]., ffar4 […]

PMCID: 5669193
PMID: 28615213
DOI: 10.1161/JAHA.117.005971

[…] upstream of the coding sequence (figure a through d). in the hhr heart, both lcn2 mrna and pre‐mrna levels were increased (figure e), suggesting a transcriptional dysregulation of lcn2 in the hhr. transcription factor affinity prediction (strap), analysis suggested that one of these snps (rs196968512) created a binding site for the enhancer, rar‐related orphan receptor a (figure b and f). , […]

TRAP institution(s)
Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany; Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
TRAP funding source(s)
Supported by the Alexander von Humboldt foundation.

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