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Protocols

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GraphProt specifications

Information


Unique identifier OMICS_02252
Name GraphProt
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Rolf Backofen <>

Publication for GraphProt

GraphProt in pipelines

 (2)
2018
PMCID: 5861125
PMID: 29559621
DOI: 10.1038/s41467-018-03575-4

[…] peaks of the nuclear isoform qki-5 were located predominantly on intronic regions, whereas peaks of qki-6 were located to a large extent on 3′-utrs as well as intronic regions (fig. ). the graphprot motif for qki-5 closely resembled the known qki core motif acuaay,, whereas the motif for qki-6 better resembled the consensus motif ayuaay identified from highly expressed par-clip read […]

2018
PMCID: 5861125
PMID: 29559621
DOI: 10.1038/s41467-018-03575-4

[…] on the merged peak regions of the full sets of jamm peaks. spearman's correlations of biological replicates based on peakachu peaks were calculated using bedtools, parallel and r (version 3.4.2)., graphprot sequence models were trained on 10,000 randomly selected peaks and roughly equal numbers of unbound sequences, using default parameters (graphprot version 1.1.3). unbound sequences […]


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GraphProt in publications

 (13)
PMCID: 5861125
PMID: 29559621
DOI: 10.1038/s41467-018-03575-4

[…] peaks of the nuclear isoform qki-5 were located predominantly on intronic regions, whereas peaks of qki-6 were located to a large extent on 3′-utrs as well as intronic regions (fig. ). the graphprot motif for qki-5 closely resembled the known qki core motif acuaay,, whereas the motif for qki-6 better resembled the consensus motif ayuaay identified from highly expressed par-clip read […]

PMCID: 5866599
PMID: 29507242
DOI: 10.1073/pnas.1721670115

[…] of the aaatt pentamer, thus further demonstrating the reproducibility of hnrnp r iclip (fig. s1d). we also used an independent approach by learning binding models on the different datasets using graphprot (). the binding model for the hnrnp r iclip dataset similarly revealed an a/u-rich consensus motif () in contrast to the model learned from the igg control iclip dataset (fig. s1e)., within […]

PMCID: 5819699
PMID: 29463232
DOI: 10.1186/s12864-018-4540-1

[…] repressor []. according to our model, pum2 prefers to bind uguaa in a paired context; i.e., binds in a double-stranded context (fig. ). our finding was further confirmed by an independent method, graphprot, on an independent dataset derived from a par-clip experiment []. the improvement in pearson correlation on in vitro binding prediction is 0.14. the auc for in vivo data improved from 0.52 […]

PMCID: 5331642
PMID: 28245811
DOI: 10.1186/s12859-017-1561-8

[…] prediction []. the other implementation of feature-level fusion is the multiple-kernel learning, which design multiple kernels for different features, and then combine them together [, ]. similarly, graphprot encodes the sequence and structure information to graph kernel to predict binding reference of rbps [].decision-level fusion. to solve the high-dimension space learning problem, decision […]

PMCID: 5300891
PMID: 28147274
DOI: 10.1016/j.celrep.2016.12.091

[…] domain shows a significant degree of freedom in the rna-interacting groove, which is maintained upon rna binding. finally, it is worth mentioning that a preliminary bioinformatics analysis using the graphprot program () (data not shown) suggests that in the ensemble of putative kh4-binding sites, the kh4 sites are more likely to engage in structural contacts than the kh3 ones, but are unlikely […]


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