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Musite specifications

Information


Unique identifier OMICS_05941
Name Musite
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 1.0.1
Stability Stable
Requirements
JRE
Registration required Yes
Maintained Yes

Versioning


No version available

Additional information


http://musite.sourceforge.net/

Information


Unique identifier OMICS_05941
Name Musite
Interface Web user interface
Restrictions to use None
Input data A protein sequence.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Additional information


http://musite.sourceforge.net/

Publication for Musite

Musite citations

 (20)
library_books

Cold and Heat Stress Diversely Alter Both Cauliflower Respiration and Distinct Mitochondrial Proteins Including OXPHOS Components and Matrix Enzymes

2018
Int J Mol Sci
PMCID: 5877738
PMID: 29547512
DOI: 10.3390/ijms19030877

[…] Phosphorylation sites were predicted by PhosPhAt v4.0 (Available online: http://phosphat.uni-hohenheim.de/; []), NetPhos v2.0, available online: (http://www.cbs.dtu.dk/services/NetPhos-2.0/; []) and MUsite v1.0 (Available online: www.musite.net; []). Methylation sites were predicted by PMes (Available online: http://bioinfo.ncu.edu.cn/inquiries_PMeS.aspx; []). The data were compared with Arabidop […]

library_books

Chlorophyte aspartyl aminopeptidases: Ancient origins, expanded families, new locations, and secondary functions

2017
PLoS One
PMCID: 5638241
PMID: 29023459
DOI: 10.1371/journal.pone.0185492

[…] tructures are conserved [, , ] (; ). The exception is AtDAP1’s Phe406, which is located in the catalytic pocket. This residue is a Tyr in AtDAP2 and P. falciparum, while it is a Leu in animals ().The Musite program predicts that several Ser and/or Thr residues may be phosphorylated in plant DAPs () []. The majority of the predicted Ser/Thr phosphorylation sites within DAPs reside within the C-term […]

library_books

Plant genome and transcriptome annotations: from misconceptions to simple solutions

2017
Brief Bioinform
PMCID: 5952960
PMID: 28062412
DOI: 10.1093/bib/bbw135

[…] In the case where one is interested in signaling, one can predict phosphorylation sites using four plant tools at the moment, namely PHOSFER [], PhosPhAt [], PlantPhos [] and Musite []. In terms of performance, the latter three tools have recently been compared, and it seemed that for serine/threonine predictions, at least in the model A. thaliana, Musite performed best. I […]

library_books

Prediction of post translational modification sites using multiple kernel support vector machine

2017
PeerJ
PMCID: 5410141
PMID: 28462053
DOI: 10.7717/peerj.3261

[…] ally occur at specific yet conserved motif in the target protein (; ; ). For example, to predict phosphorylation sites, a number of local sequence based tools have been developed, such as GPS 2.0 (), Musite (), PhosphoSVM (), NetPhos () and KinasePhos 2.0 (). Besides phosphorylation, much effort also has been contributed to developing bioinformatics tools to identify other PTM sites. developed a […]

library_books

Genome wide characterisation and expression profile of the grapevine ATL ubiquitin ligase family reveal biotic and abiotic stress responsive and development related members

2016
Sci Rep
PMCID: 5133618
PMID: 27910910
DOI: 10.1038/srep38260

[…] s/TargetP/) and Protein Prowler Subcellular Localisation v1.2 (http://bioinf.scmb.uq.edu.au:8080/pprowler_webapp_1-2/) with a cut-off of probability of 0.5. Phosphorylation sites were predicted using MUsite v1.0 (http://musite.sourceforge.net/). […]

call_split

RF Phos: A Novel General Phosphorylation Site Prediction Tool Based on Random Forest

2016
Biomed Res Int
PMCID: 4811047
PMID: 27066500
DOI: 10.1155/2016/3281590
call_split See protocol

[…] d. These methods, which are based on various learning methods, are described briefly below. NetPhos is a general phosphosite predictor that uses structural information as features to train an ANN []. Musite integrates local sequence similarities of known phosphorylation sites, protein disorder scorers, and amino acid frequencies as features to train the support vector classifier []. The method dev […]

Citations

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Musite institution(s)
Departments of Computer Science and Biochemistry University of Missouri, MO, Columbia, USA; C. S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Center for Computational Biology and Bioinformatics, Indiana University Schools of Medicine and Informatics, Indianapolis, IN, USA
Musite funding source(s)
Supported by National Institutes of Health Grant R21/R33 GM078601, and by National Science Foundation-Plant Genome Research Program Grant DBI-0604439.

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