Feature-Based Classification of Amino Acid Substitutions outside Conserved Functional Protein Domains
Joint Authors
Gemovic, Branislava
Perovic, Vladimir
Glisic, Sanja
Veljkovic, Nevena
Source
Issue
Vol. 2013, Issue 2013 (31 Dec. 2013), pp.1-10, 10 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2013-11-17
Country of Publication
Egypt
No. of Pages
10
Main Subjects
Medicine
Information Technology and Computer Science
Abstract EN
There are more than 500 amino acid substitutions in each human genome, and bioinformatics tools irreplaceably contribute to determination of their functional effects.
We have developed feature-based algorithm for the detection of mutations outside conserved functional domains (CFDs) and compared its classification efficacy with the most commonly used phylogeny-based tools, PolyPhen-2 and SIFT.
The new algorithm is based on the informational spectrum method (ISM), a feature-based technique, and statistical analysis.
Our dataset contained neutral polymorphisms and mutations associated with myeloid malignancies from epigenetic regulators ASXL1, DNMT3A, EZH2, and TET2.
PolyPhen-2 and SIFT had significantly lower accuracies in predicting the effects of amino acid substitutions outside CFDs than expected, with especially low sensitivity.
On the other hand, only ISM algorithm showed statistically significant classification of these sequences.
It outperformed PolyPhen-2 and SIFT by 15% and 13%, respectively.
These results suggest that feature-based methods, like ISM, are more suitable for the classification of amino acid substitutions outside CFDs than phylogeny-based tools.
American Psychological Association (APA)
Gemovic, Branislava& Perovic, Vladimir& Glisic, Sanja& Veljkovic, Nevena. 2013. Feature-Based Classification of Amino Acid Substitutions outside Conserved Functional Protein Domains. The Scientific World Journal،Vol. 2013, no. 2013, pp.1-10.
https://search.emarefa.net/detail/BIM-1013200
Modern Language Association (MLA)
Gemovic, Branislava…[et al.]. Feature-Based Classification of Amino Acid Substitutions outside Conserved Functional Protein Domains. The Scientific World Journal No. 2013 (2013), pp.1-10.
https://search.emarefa.net/detail/BIM-1013200
American Medical Association (AMA)
Gemovic, Branislava& Perovic, Vladimir& Glisic, Sanja& Veljkovic, Nevena. Feature-Based Classification of Amino Acid Substitutions outside Conserved Functional Protein Domains. The Scientific World Journal. 2013. Vol. 2013, no. 2013, pp.1-10.
https://search.emarefa.net/detail/BIM-1013200
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1013200