AFP-SRC: Identification of Antifreeze Proteins Using Sparse Representation Classifier
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Species living in the extreme cold environment fight against the harsh conditions by virtue of antifreeze proteins (AFPs), that manipulates the freezing mechanism of water in more than one way. This amazing nature of AFP turns out to be extremely useful in a number of industrial and medical applications. The lack of similarity in their structure and sequence makes their prediction an arduous task and identifying them experimentally in the wet-lab is time consuming and expensive. In this research, we propose a computational framework for the prediction of AFPs which is essentially based on a sample-specific classification method using the sparse reconstruction. A linear model and an over-complete dictionary matrix of known AFPs is used to predict sparse class-label vector which provides sample-association score. Delta-rule is applied for the reconstruction of two pseudo-samples using lower and upper parts of sample-association vector and based on the minimum recovery score, class labels are assigned. We compare our approach with contemporary methods on a standard dataset and the proposed method is found to outperform in terms of Matthews correlation coefficient and Youden's index. The MATLAB implementation of proposed method is available at author's github page https://github.com/Shujaat123/AFP-SRC.
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