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Negative GO Annotations NegGOA

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Selects negative examples of GO annotations using ontology structure. NegGOA takes advantage of the ontology structure, available annotations and potentiality of additional annotations of a protein to choose negative examples of the protein. We compare this tool with other negative examples selection algorithms and find that NegGOA produces much fewer false negatives than them. We incorporate the selected negative examples into an efficient function prediction model to predict the functions of proteins in Yeast, Human, Mouse and Fly. It also demonstrates improved accuracy than these comparing algorithms across various evaluation metrics. In addition, NegGOA is less suffered from incomplete annotations of proteins than these comparing methods.

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NegGOA forum

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NegGOA classification

  • Animals
    • Drosophila melanogaster
    • Homo sapiens
    • Mus musculus
  • Fungi
    • Saccharomyces cerevisiae

NegGOA specifications

Software type:
Package/Module
Restrictions to use:
Academic or non-commercial use
Output data:
Negative annotations of a protein
Programming languages:
MATLAB, R
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface
Input data:
Ontology structure, available annotations and potentiality of additional annotations of a protein
Operating system:
Unix/Linux, Mac OS, Windows
License:
Artistic License version 2.0
Version:
1.0
Maintained:
Yes

NegGOA distribution

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NegGOA support

Maintainer

  • Guoxian Yu <>

Credits

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Publications

Institution(s)

College of Computer and Information Science, Southwest University, Chongqing, China; Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China

Funding source(s)

Natural Science Foundation of China (No. 61402378); Natural Science Foundation of CQ CSTC (No. cstc2014jcyjA40031); Fundamental Research Funds for the Central Universities of China (2362015XK07, XDJK2016B009 and XDJK2016D021)

Link to literature

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