Abstract
A novel approach to signal peptide identification is presented. We use an evolutionary algorithm for automatic evolution of classification programs, so-called programmatic motifs. The variant of evolutionary algorithm used is called genetic programming where a population of solution candidates in the form of full computer programs is evolved, based on training examples consisting of signal peptide sequences. The method is compared with a previous work using artificial neural network (ANN) approaches. Some advantages compared to ANNs are noted. The programmatic motif can perform computational tasks beyond that of feed-forward neural networks and has also other advantages such as readability. The best motif evolved was analyzed and shown to detect the h-region of the signal peptide. A powerful parallel computer cluster was used for the experiment.
Highlights
The huge and growing amount of unanalyzed data present in genetic research creates a demand for automatic methods for classification of proteins and protein properties
Classification rules for the processing of amino acid sequences can be obtained either by human design or by a mechanical process, the latter often through the use of machinelearning algorithms
genetic programming (GP) is a branch of evolutionary algorithms where computer programs are evolved from first principles to solve a problem specified by a fitness function
Summary
The huge and growing amount of unanalyzed data present in genetic research creates a demand for automatic methods for classification of proteins and protein properties. Signal peptides are referred to as the address tags within the cell since they control the transport of proteins through the secretory pathway, the mechanism that moves proteins through cell membranes. These proteins are produced by ribosomes in the cytoplasm but the produced peptide does not fold to become a protein at this stage. The first part of the peptide, the signal peptide, attaches itself to a translocon in the membrane. This binding opens a channel and the peptide starts to transport itself through the translocon channel. The protein’s peptide is free and can fold itself to become an active, or mature, protein
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