SVM-SEQ protocols

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SVM-SEQ specifications

Information


Unique identifier OMICS_10843
Name SVM-SEQ
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Protein sequence
Input format FASTA
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Yang Zhang <>

Information


Unique identifier OMICS_10843
Name SVM-SEQ
Interface Web user interface
Restrictions to use None
Input data Protein sequence
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Yang Zhang <>

Publication for SVM-SEQ

SVM-SEQ in pipeline

2009
PMCID: 2689239
PMID: 19419562
DOI: 10.1186/1472-6807-9-28

[…] study. moreover, if only the 15 new fold casp7 targets are considered, our method achieves an average accuracy of 37%, which is much better than that of the majority voting method, svm-lomets, svm-seq, and sam-t06. these methods demonstrate an average accuracy of 13.0%, 10.8%, 25.8% and 21.2%, respectively., reducing server correlation and optimally combining independent latent servers […]


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SVM-SEQ in publications

 (3)
PMCID: 3166291
PMID: 21912654
DOI: 10.1371/journal.pone.0023947

[…] a straightforward svm using a linear kernel, and svm-rbf, which uses a (non-linear) radial basis function kernel. here we describe results from svm-lin, svm-rbf, and an svm-rbf variant called svm-seq. svm-lin is simpler, using a linear kernel in the original input space, and allows straightforward determination from a trained classifier of the features most important for classification. […]

PMCID: 3078102
PMID: 21429187
DOI: 10.1186/1471-2105-12-83

[…] methodology. table summarizes results (see also figure that shows only ilp models with best performance). ilp-dt models did not reach good performance on sfull and s30 databases (see methods). ilp-svm-seq-alncons-alnpc models outperformed all other ilp methods for both databases., some logical rules learned from "glucocorticoid receptor-like (dna-binding domain)" sequences and their alignment […]

PMCID: 2689239
PMID: 19419562
DOI: 10.1186/1472-6807-9-28

[…] state-of-the-art threading programs as inputs. lomets predicts contacts by attempting to select the best input model., recently, two support vector machines (svms) based contact prediction methods, svm-seq and svm-lomets, have been proposed by wu et al. []. svm-seq only takes sequence-derived information into consideration, whereas svm-lomets, a consensus method, is based on structural […]


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SVM-SEQ institution(s)
Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, Lawrence, KS, USA
SVM-SEQ funding source(s)
The project is supported by KU Start-up Fund 06194.

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