Sueoka and Lobry declared respectively that, in the absence of bias between the two DNA strands for mutation and selection, the base composition within each strand should be A=T and C=G (this state is called Parity Rule type 2, PR2). However, the genome sequences of many bacteria, vertebrates and viruses showed asymmetries in base composition and gene direction. To determine the relationship of base composition skews with replication orientation, gene function, codon usage biases and phylogenetic evolution, in this paper a program called DNAskew was developed for the statistical analysis of strand asymmetry and codon composition bias in the DNA sequence. In addition, the program can also be used to predict the replication boundaries of genome sequences. The method builds on the fact that there are compositional asymmetries between the leading and the lagging strand for replication. DNAskew was written in Perl script language and implemented on the LINUX operating system. It works quickly with annotated or unannotated sequences in GBFF (GenBank flatfile) or fasta format. The source code is freely available for academic use at http://www.epizooty.com/pub/stat/DNAskew.
In addition to the central role of ribosome biogenesis, the human ribosomal protein S15 (RPS15) has extraribosomal roles that include its association with a congenital disease and a few types of cancer. However, current knowledge of its functions in the context of extra-ribosomal activities remains fragmented. An approach to gain insights into the interaction between RPS15 and possible protein partners is via Bioinformatics strategies. Based on the sequence-to-structure-to-function paradigm, structural data of a protein can be computationally analysed to derive logical interacting partners. This method can include three-dimensional model construction, structural neighbour prediction, and molecular docking analysis. By using this approach, we have constructed RPS15 3D-structural models that have allowed the prediction of 23 structural neighbours. Of these, two that are from human origin were further analysed and only one have logical prospect of binary protein -protein interactions. Further analysis of this structural neighbour revealed 7 candidate docking partners. From these, our molecular docking analysis demonstrated two most logical dock models of interactions between RPS15 with two different domains of the Fragile X Mental Retardation Protein 1 (FMRP1) protein. Hence, we have provided in silico evidence of de novo protein-protein interaction between RPS15 and the Fragile X Mental Retardation Protein 1 (FMRP1).
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