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kmer-SVM specifications

Information


Unique identifier OMICS_00484
Name kmer-SVM
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Michael A. Beer <>

Publications for kmer-SVM

kmer-SVM in publications

 (7)
PMCID: 5755920
PMID: 29267279
DOI: 10.1371/journal.pgen.1007123

[…] against the prevailing view of dna methylation in vertebrates., statistical association between medaka genomic sequences and local methylation states was modelled using support vector machine (kmer-svm []). hypomethylated and hypermethylated genomic loci (a.k.a. hypomethylated domains, “hypomds”, and hypermethylated domains, “hypermds”, respectively) at the blastula stage (stage 11 […]

PMCID: 5773911
PMID: 29219068
DOI: 10.1186/s12859-017-1878-3

[…] problem, computational approaches have been proposed to conduct in silicon prediction of enhancers by using dna sequences. to mention a few, lee et al. developed a computational framework called kmer-svm based on the support vector machine (svm) to discriminate mammalian enhancers from background sequences []. they found that some predictive k-mer features are enriched in enhancers […]

PMCID: 5870572
PMID: 28881969
DOI: 10.1093/bioinformatics/btx234

[…] methods have been proposed to identify functional regions, which mainly fall into two classes. one class is the kmer-based methods, where k-mers are defined as oligomers of length k. for example, kmer-svm provided a support vector machine (svm) framework for mammalian enhancers discrimination based on k-mer features (). shortly after kmer-svm was proposed, gkm-svm introduced an alternative […]

PMCID: 5374684
PMID: 28361702
DOI: 10.1186/s12918-017-0389-1

[…] single nucleotide variants and evaluate the impact of single nucleotide polymorphism (snp). in a series of experiments, our kmerforest method outperforms the existing state-of-the-art approach, kmer-svm [], in a variety of cell lines. based on this model, we introduced a score called the mean decrease accuracy (mda) to evaluate input features. we then calculated mda scores […]

PMCID: 4814916
PMID: 27030570
DOI: 10.1038/srep23934

[…] a widely used feature considering the local sequence order information along the dna sequences. gkm is an improvement of k-mer by introducing the gaps into k-mers. for comparison, a predictor called kmer-svm is constructed based on k-mers. the kmer-svm can be viewed as a special case of gkm-svm without gaps. therefore, the implementation of kmer-svm is the same as that of svm-gkm except […]


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kmer-SVM institution(s)
McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA

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