iSS-PseDNC: Identifying Splicing Sites Using Pseudo Dinucleotide Composition

Abstract

In eukaryotic genes, exons are generally interrupted by introns. Accurately removing introns and joining exons together are essential processes in eukaryotic gene expression. With the avalanche of genome sequences generated in the postgenomic age, it is highly desired to develop automated methods for rapid and effective detection of splice sites that play important roles in gene structure annotation and even in RNA splicing. Although a series of computational methods were proposed for splice site identification, most of them neglected the intrinsic local structural properties. In the present study, a predictor called “iSS-PseDNC” was developed for identifying splice sites. In the new predictor, the sequences were formulated by a novel feature-vector called “pseudo dinucleotide composition” (PseDNC) into which six DNA local structural properties were incorporated. It was observed by the rigorous cross-validation tests on two benchmark datasets that the overall success rates achieved by iSS-PseDNC in identifying splice donor site and splice acceptor site were 85.45% and 87.73%, respectively. It is anticipated that iSS-PseDNC may become a useful tool for identifying splice sites and that the six DNA local structural properties described in this paper may provide novel insights for in-depth investigations into the mechanism of RNA splicing.

iTIS-PseTNC: A sequence-based predictor for identifying translation initiation site in human genes using pseudo trinucleotide composition

“…To make these metrics in a more intuitive and easier-to-understand formulation, let us use the following equations to represent them as done in a series of recent publications (see, e.g., [14,15,68])…”

Pse-in-One 2.0: An Improved Package of Web Servers for Generating Various Modes of Pseudo Components of DNA, RNA, and Protein Sequences

“…"Distance Pair" method incorporates the amino acid distance pair coupling information and the amino acid reduced alphabet profile into the general pseudo amino acid composition (PseAAC) [108] vector, which is very useful for analysing DNA-binding proteins [15,170,189,275]. PDT is the abbreviation for "physicochemical distance transformation", which can incorporate considerable sequence-order information or important patterns of protein/peptide sequences into Pseudo components [28], which is very useful for conducting various proteome analyses [17, 23, 215-217, 224, 225, 231, 235, 276-289] and genome analysis as well [216,218,220,223,229,255,277,290].…”

Identification of Heat Shock Protein families and J-protein types by incorporating Dipeptide Composition into Chou's general PseAAC

“…SVM is the most popular and extensively used learning algorithm in the area of Machine learning, pattern recognition and bioinformatics [29,[74][75][76]. It is based on statistical theory.…”

“…It is based on statistical theory. It was first introduced by Cortes and Vapnik in 1995 [29,74]. Later on, it was modified in 1999 [76].…”

“…In addition, Feng et al, also developed the first automated method for the discrimination of J-Protein types and obtained the overall accuracy of 94% [16]. As summarized and demonstrated by a series of publication [2,[24][25][26][27][28][29][30][31][32], in compliance with Chou's 5-step rule [33], to develop a convenient sequence-based prediction model for a biological system, the following procedures are necessary to consider: the first step is to choose or establish a valid benchmark dataset in order to train and test the predictor; the second step is to express the biological sequences into effective mathematical formula that can truly represent their intrinsic correlation with the target to be predicted; the third step is to introduce or develop a powerful learning algorithm; the fourth step A c c e p t e d M a n u s c r i p t 6 is to perform statistical cross-validation tests to assess the performance of the predictor; and finally develop a user-friendly and publicly accessible web-server for the predictor that is accessible to the public.…”