The complexities of genome analysis, the Retroid agent perspective.
BACKGROUND
The sequences of Retroid agents from a wide diversity of organisms constitute the largest set of complete genomes currently available for the study of genomic architecture and the transfer of information within and between organisms. These agents are ubiquitous in Eukaryotes, comprising 50-90% of the genomic information in some cases.


RESULTS
Analyses conducted for over a decade illustrate that Retroid agents are engaged in a wide spectrum of molecular evolutionary events. A description of these complexities is presented as a three parameter conceptual framework that considers type, size, and mechanism of events that contribute to the evolution of genes, genomes, and organisms. The results of new data mining studies further illustrate the complexity of the network of relationships among and between Retroid agents and other organisms. A hidden Markov model construction strategy is presented that generates a multiple alignment more similar to those refined by human experts.


BACKGROUND
mars@parvati.msu.montana. edu
McClure
M A
MA
Department of Microbiology, Montana State University, Bozeman, USA. mars@parvati.msu.montana.edu
D000818:Animals; D019195:Badnavirus / Q000235:genetics; D017796:Caulimovirus / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D019143:Evolution, Molecular; D016679:Genome, Viral; D015613:Hepadnaviridae / Q000235:genetics; D006801:Humans; D012313:RNA / Q000032:analysis; D012190:Retroviridae / Q000235:genetics
D004251:DNA Transposable Elements; D012313:RNA