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<p>Abstract</p> <p>Background</p> <p>The completed genome sequences of the malaria parasites <it>P. falciparum</it>, <it>P. y. yoelii </it>and <it>P. vivax </it>have revealed some unusual features. <it>P. falciparum </it>contains the most AT rich genome sequenced so far – over 90% in some regions. In comparison, <it>P. y. yoelii </it>is ~77% and <it>P. vivax </it>is ~55% AT rich. The evolutionary reasons for these findings are unknown. Mobile genetic elements have a considerable impact on genome evolution but a thorough investigation of these elements in <it>Plasmodium </it>has not been undertaken. We therefore performed a comprehensive genome analysis of these elements and their derivatives in the three <it>Plasmodium </it>species.</p> <p>Results</p> <p>Whole genome analysis was performed using bioinformatic methods. Forty potential protein encoding sequences with features of transposable elements were identified in <it>P. vivax</it>, eight in <it>P. y. yoelii </it>and only six in <it>P. falciparum</it>. Further investigation of the six open reading frames in <it>P. falciparum </it>revealed that only one is potentially an active mobile genetic element. Most of the open reading frames identified in all three species are hypothetical proteins. Some represent annotated host proteins such as the putative telomerase reverse transcriptase genes in <it>P. y. yoelii </it>and <it>P. falciparum</it>. One of the <it>P. vivax </it>open reading frames identified in this study demonstrates similarity to telomerase reverse transcriptase and we conclude it to be the orthologue of this gene.</p> <p>Conclusion</p> <p>There is a divergence in the frequencies of mobile genetic elements in the three <it>Plasmodium </it>species investigated. Despite the limitations of whole genome analytical methods, it is tempting to speculate that mobile genetic elements might have been a driving force behind the compositional bias of the <it>P. falciparum </it>genome.</p>