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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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Versioning


No version available

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 citations

 (7)
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Investigation of single and synergic effects of NLRC5 and PD L1 variants on the risk of colorectal cancer

2018
PLoS One
PMCID: 5800657
PMID: 29408916
DOI: 10.1371/journal.pone.0192385
call_split See protocol

[…] nvestigate 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 affected […]

call_split

Polymorphisms in FFAR4 (GPR120) Gene Modulate Insulin Levels and Sensitivity after Fish Oil Supplementation

2017
PMCID: 5748627
PMID: 29113108
DOI: 10.3390/jpm7040015
call_split See protocol

[…] ah (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 [,,]. […]

library_books

Plasma Triglyceride Levels May Be Modulated by Gene Expression of IQCJ, NXPH1, PHF17 and MYB in Humans

2017
Int J Mol Sci
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 […]

call_split

Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations

2016
Cell
PMCID: 5075285
PMID: 27768888
DOI: 10.1016/j.cell.2016.09.024
call_split See protocol

[…] dules downregulated (modules 5–9), or containing similarly expressed genes across conditions (module 10), were enriched in functions such as RNA processing and translational termination (B).Using the transcription factor affinity prediction (TRAP) method (), we found that the annotated promoter regions of the genes within each module were enriched in binding motifs for specific transcription facto […]

library_books

In silico identification of enhancers on the basis of a combination of transcription factor binding motif occurrences

2016
Sci Rep
PMCID: 5007594
PMID: 27582178
DOI: 10.1038/srep32476

[…] (PWM). In this work, a total of 1,422 PWMs were collected from Cistrome and the TRANSFAC track in the UCSC Genome Browser. For a given sequence, the ability of a TF to bind DNA was represented by the transcription factor affinity prediction (TRAP) score, which was calculated according to the transcription factor motif PWM by the TRAP program. The parameters of the TRAP program used default values. […]

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Identification and characterization of the novel Col10a1 regulatory mechanism during chondrocyte hypertrophic differentiation

2014
PMCID: 4649528
PMID: 25321476
DOI: 10.1038/cddis.2014.444
call_split See protocol

[…] http://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promoinit.cgi?dirDB=TF_8.3. The searching result of potential TFBS will be displayed through a graphical interface or as a downloadable text file. (3) Transcription factor affinity prediction (TRAP): TRAP is used to predict which TFs are susceptible to bind a promoter with highest affinity. TRAP uses the TRANSFAC database and the searching result is […]

Citations

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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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