New phylogenetic venues opened by a novel implementation of the DNAml algorithm

n-gram-based classification and unsupervised hierarchical clustering of genome sequences

In this paper we address the problem of automated classification of isolates, i.e., the problem of determining the family of genomes to which a given genome belongs. Additionally, we address the problem of automated unsupervised hierarchical clustering of isolates according only to their statistical substring properties. For both of these problems we present novel algorithms based on nucleotide n-grams, with no required preprocessing steps such as sequence alignment. Results obtained experimentally are very positive and suggest that the proposed techniques can be successfully used in a variety of related problems. The reported experiments demonstrate better performance than some of the state-of-the-art methods. We report on a new distance measure between n-gram profiles, which shows superior performance compared to many other measures, including commonly used Euclidean distance.

Identification of two CRF11-cpx genomes and two preliminary representatives of a new circulating recombinant form (CRF13-cpx) of HIV type 1 in Cameroon

Recombination is an efficient mechanism of HIV-1 to generate genetic variability. Some of the recombinant forms of HIV-1 that have been described are of epidemic importance, and they are referred to as circulating recombinant forms (CRFs). In this study, we characterized four HIV-1 isolates from Cameroon that had previously been classified as subtype J in the protease gene and as subtype A in the env C2-V5 region. Analyses of the nearly complete genomes revealed that two of the samples (95CM-1816 and 96CM-4496) had the same recombinant structure as CRF11-cpx. The two remaining samples (96CM-1849 and 96CM-4164) constituted a new recombinant virus variant with genomic regions identified as subtypes A, G, J, and CRF01-AE. This mosaic virus structure was found in two individuals who had no direct epidemiological relationship, and may thus represent a new CRF. The fragments that were classified as subtype J in the new recombinant form were more related to subtype J regions of the CRF11-cpx sequences than to the reference strains of subtype J. The complex structures of CRF11-cpx and our new recombinant form, which are both the result of at least four recombination events, exemplify the coming difficulties in characterizing the internal relationships and origins of future recombinant HIV-1 strains. The new recombinant structure has been designated CRF13-cpx in the Los Alamos HIV Sequence Database.