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Inferring biological basis about psychrophilicity by interpreting the rules generated from the correctly classified input instances by a classifier

Paper ID Volume ID Publish Year Pages File Format Full-Text
15084 1374 2014 6 PDF Available
Title
Inferring biological basis about psychrophilicity by interpreting the rules generated from the correctly classified input instances by a classifier
Abstract

•Enhanced classification of psychrophilic proteins by rotation forest.•Rule extraction from correctly classified sequences.•Validation of generated rules on structural data.•Biological interpretation of rules.•Ranking of amino acids according to their discriminative ability.

Organisms thriving at extreme cold surroundings are called as psychrophiles and they present a wealth of knowledge about sequence adjustments in proteins that had occurred during the adaptation to low temperatures. In this paper, we propose a new cascading model to investigate the basis for psychrophilicity. In this model, a superior classifier was used to discriminate psychrophilic from mesophilic protein sequences, and then the PART rule generating algorithm was applied on the input instances that are correctly classified by the classifier, to generate human interpretable rules. These derived rules were further validated on a structural dataset and finally analyzed to discover the underlying biological basis about the psychrophilicity. In this study, we have used one of the key features of psychrophilic proteins accountable for remaining functional in extreme cold temperature surroundings i.e., global patterns of amino acid composition as the input features. The rotation forest classifier outperformed all the other classifiers with maximum accuracy of 70.5% and maximum AUC of 0.78. The effect of sequence length on the classification accuracy was also investigated. The analysis of the derived rules and interpretation of the analyzed results had revealed some interesting phenomena such as the amino acids A, D, G, F, and S are over-represented, and T is under-represented in psychrophilic proteins. These findings augment the existing domain knowledge for psychrophilic sequence features.

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Keywords
Biologically interpretable rules; Cold adaptation; Amino acid composition patterns; Rotation forest; PART rule induction method
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Inferring biological basis about psychrophilicity by interpreting the rules generated from the correctly classified input instances by a classifier
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 53, Part B, December 2014, Pages 198–203
Authors
, ,
Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us