DomCut protocols

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DomCut specifications

Information


Unique identifier OMICS_07072
Name DomCut
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Mikita Suyama <>

Publication for DomCut

DomCut in pipeline

2008
PMCID: 2259413
PMID: 18315843
DOI: 10.1186/1471-2105-9-S1-S12

[…] and pre-processing datasets., (2) obtain protein structural information such as pssm, solvent accessibility, secondary structure and linker index by utilising psi-blast [], accpro [], sspro [] and domcut []., (3) the information obtained in (2) was combined and normalised to fall in the interval [-1, 1] to be fed into networks., (4) assign target levels: positive (1) for boundary residues […]


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DomCut in publications

 (12)
PMCID: 5300222
PMID: 28182704
DOI: 10.1371/journal.pone.0171944

[…] such as prediction of signal peptides (signalp-4.1) [], transmembrane regions (tmhmm-2.0) [], non-classical secretion proteins (secretomep-2.) [], functional and structural domains (interpro [] and domcut []) (). the rationale of expressing the protein in fragments was due to: 1) enhanced probability of expressing the native protein structure, 2) expressing the protective part of the protein, […]

PMCID: 5291697
PMID: 28168220
DOI: 10.1126/sciadv.1602350

[…] furthermore, mev-edm n was submitted to pondr-fit () and disopred () for disorder predictions. to quantitatively assess the consensus of all algorithms, average values of globplot2, foldindex, and domcut () were transformed to positive integers, and positive output scores of all algorithms were normalized for identical hit cutoff values. all average scores were then transformed to a scale of 0 […]

PMCID: 4621036
PMID: 26502173
DOI: 10.1371/journal.pone.0141541

[…] methods mainly focused on domain number and boundary prediction. dgs[] guesses the domain number and further infers domain boundaries by predicting the size and the segment number of domains. domcut[] predicts inter-domain linker regions based solely on amino acid sequence composition information. pfam[–], everest[,] adda[], and fiefdom[] focus on domain boundaries prediction based […]

PMCID: 4566126
PMID: 26359642
DOI: 10.1038/srep14079

[…] be noted, however, that the domain predictive algorithms used in the two studies were different. domain assignment in the previous work was based on a pfam homology-based algorithm, whereas the domcut algorithm employed in this study utilizes sequence–specific features for domain prediction. as a result, domain definition is different in the two algorithms, and the outcomes […]

PMCID: 4290662
PMID: 25521329
DOI: 10.1186/1471-2105-15-S16-S8

[…] can be classified into (i) statistical-based, (ii) alignment/homology-based and (iii) machine-learning (ml)-based methods. dom-cut [] is one of the typical early day's statistical-based methods. domcut predicts inter-domain linker regions based on the differences in aa compositions between domain and linker regions in a protein sequence. domcut considers a region or segment in a sequence […]


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DomCut institution(s)
Laboratory of DNA Technology, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan

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