Empirical Relationship between Intra-Purine and Intra-Pyrimidine Differences in Conserved Gene Sequences

DNA sequences seen in the normal character-based representation appear to have a formidable mixing of the four nucleotides without any apparent order. Nucleotide frequencies and distributions in the sequences have been studied extensively, since the simple rule given by Chargaff almost a century ago that equates the total number of purines to the pyrimidines in a duplex DNA sequence. While it is difficult to trace any relationship between the bases from studies in the character representation of a DNA sequence, graphical representations may provide a clue. These novel representations of DNA sequences have been useful in providing an overview of base distribution and composition of the sequences and providing insights into many hidden structures. We report here our observation based on a graphical representation that the intra-purine and intra-pyrimidine differences in sequences of conserved genes generally follow a quadratic distribution relationship and show that this may have arisen from mutations in the sequences over evolutionary time scales. From this hitherto undescribed relationship for the gene sequences considered in this report we hypothesize that such relationships may be characteristic of these sequences and therefore could become a barrier to large scale sequence alterations that override such characteristics, perhaps through some monitoring process inbuilt in the DNA sequences. Such relationship also raises the possibility of intron sequences playing an important role in maintaining the characteristics and could be indicative of possible intron-late phenomena

Mapping Biomolecular Sequences: Graphical Representations - Their Origins, Applications and Future Prospects

: The exponential growth in the depositories of biological sequence data has generated an urgent need to store, retrieve and analyse the data efficiently and effectively for which the standard practice of using alignment procedures are not adequate due to high demand on computing resources and time. Graphical representation of sequences has become one of the most popular alignment-free strategies to analyse the biological sequences where each basic unit of the sequences – the bases adenine, cytosine, guanine and thymine for DNA/RNA, and the 20 amino acids for proteins – are plotted on a multi-dimensional grid. The resulting curve in 2D and 3D space and the implied graph in higher dimensions provide a perception of the underlying information of the sequences through visual inspection; numerical analyses, in geometrical or matrix terms, of the plots provide a measure of comparison between sequences and thus enable study of sequence hierarchies. The new approach has also enabled studies of comparisons of DNA sequences over many thousands of bases and provided new insights into the structure of the base compositions of DNA sequences. In this article we review in brief the origins and applications of graphical representations and highlight the future perspectives in this field. </jats:sec

A Brief Review of Computer-Assisted Approaches to Rational Design of Peptide Vaccines

The growing incidences of new viral diseases and increasingly frequent viral epidemics have strained therapeutic and preventive measures; the high mutability of viral genes puts additional strains on developmental efforts. Given the high cost and time requirements for new drugs development, vaccines remain as a viable alternative, but there too traditional techniques of live-attenuated or inactivated vaccines have the danger of allergenic reactions and others. Peptide vaccines have, over the last several years, begun to be looked on as more appropriate alternatives, which are economically affordable, require less time for development and hold the promise of multi-valent dosages. The developments in bioinformatics, proteomics, immunogenomics, structural biology and other sciences have spurred the growth of vaccinomics where computer assisted approaches serve to identify suitable peptide targets for eventual development of vaccines. In this mini-review we give a brief overview of some of the recent trends in computer assisted vaccine development with emphasis on the primary selection procedures of probable peptide candidates for vaccine development

Investigations on Evolutionary Changes in Base Distributions

Motivation. We had observed that 2D graphical plots of DNA sequences show apparently systematic variations among members of families of gene sequences and reported these to be due to evolutionary changes. Investigations of phylogenetic relationships between species through studies of gene sequences has been one of the prime areas of interest to molecular biologists. While questions such as rate of mutational changes in DNA sequences have been investigated extensively, attention is being given recently to changes in base distribution within such sequences. Roman–Roldan et al has shown that complexity of base organization in intron segments increases with evolution. Method. We use the 2D graphical representation method to map the DNA sequences and use four numerical techniques to quantitatively measure the differences observed in the different gene sequences. Results. We report here our investigations using a graphical technique for DNA sequence representation and related analyses for conserved gene sequences such as kinetoplasts, heat shock proteins, globins and others

2D graphical representations of three histone H4 sequences: Wheat (brown), maize (pink) and chicken (blue).

<p>The three plots can be seen to have similarities in shape.</p