HIV mutates at very high rates, allowing the rapid generation of potential escape mutations, which can lead to immune evasion. On top of the high rate mutation, recombination, the exchange of genetic information between two genomes, can generate new variants by breaking up or bringing together mutations. Intersubtype recombination has played a major role in the evolution of the HIV/AIDS pandemic.

A non-random distribution of the breakpoints was revealed by using bioinformatics tools. Data sets were obtained from Los Alamos HIV Sequence Database. Specifically we have tested whether there is a correlation between the distribution of the recombinant breakpoints identified in these data sets with (1) genomic sequence diversity, (2) regions identified as recombinant "hot" and "cold" spots from experimental studies, (3) predicted locations of secondary RNA structure, and (4) the predicted locations of positively selected sites.

People are not satisfied with only knowing existence of recombination anymore. More details about existing recombination are required, for example, the location where recombinations occur which is known as breakpoint. I have developed four breakpoint detection tools.

4-SIS
Parti-on (Will be published soon)
Frag-Dist
TOD (submitted to Bioinformatics)
More tools can be accessed via the list maintained by us.

Details will be published soon