ABSTRACT
In genome analysis, k-mer-based comparison methods have become standard tools. However, even though they are able to deliver reliable results, other algorithms seem to work better in some cases. To improve k-mer-based DNA sequence analysis and comparison, we successfully checked whether adding positional resolution is beneficial for finding and/or comparing interesting organizational structures. A simple but efficient algorithm for extracting and saving local k-mer spectra (frequency distribution of k-mers) was developed and used. The results were analyzed by including positional information based on visualizations as genomic maps and by applying basic vector correlation methods. This analysis was concentrated on small word lengths (1 ≤ k ≤ 4) on relatively small viral genomes of Papillomaviridae and Herpesviridae, while also checking its usability for larger sequences, namely human chromosome 2 and the homologous chromosomes (2A, 2B) of a chimpanzee. Using this alignment-free analysis, several regions with specific characteristics in Papillomaviridae and Herpesviridae formerly identified by independent, mostly alignment-based methods, were confirmed. Correlations between the k-mer content and several genes in these genomes have been found, showing similarities between classified and unclassified viruses, which may be potentially useful for further taxonomic research. Furthermore, unknown k-mer correlations in the genomes of Human Herpesviruses (HHVs), which are probably of major biological function, are found and described. Using the chromosomes of a chimpanzee and human that are currently known, identities between the species on every analyzed chromosome were reproduced. This demonstrates the feasibility of our approach for large data sets of complex genomes. Based on these results, we suggest k-mer analysis with positional resolution as a method for closing a gap between the effectiveness of alignment-based methods (like NCBI BLAST) and the high pace of standard k-mer analysis.
ABSTRACT
In recent years, studies have shown that there are many similarities between comets and asteroids. In some cases, it cannot even be determined to which of these groups an object belongs. This is especially true for objects found beyond the main asteroid belt. Because of the lack of comet fragments, more progress has been made concerning the chemical composition of asteroids. In particular, the SMASSII classification establishes a link between the reflecting spectra and chemical composition of asteroids and meteorites. To find clues for the chemical structure of comets, the parameters of all known asteroids of the SMASSII classification were compared to those of comet groups like the Encke-type comets, the Jupiter-family comets, and the Halley-type comets, as well as comet-like objects like the damocloids and the centaurs. Fifty-six SMASSII objects similar to comets were found and are categorized as comet-like asteroids in this work. Aside from the chemistry, it is assumed that the available energy on these celestial bodies plays an important role concerning habitability. For the determination of the available energy, the effective temperature was calculated. Additionally, the size of these objects was considered in order to evaluate the possibility of a liquid water core, which provides an environment that is more likely to support processes necessary to create the building blocks of life. Further study of such objects could be notable for the period of the Late Heavy Bombardment and could therefore provide important implications for our understanding of the inner workings of the prebiotic evolution within the Solar System since the beginning.
