BMC Genomics 2006, 7:282 http://www.biomedcentral.com/1471-2164/7/282 The finding that the putative RIP machinery is represented in the P. falciparum genome lends support to the first hypothesis. The second hypothesis is based on findings that various MGEs may require specific recognition sequences as potential sites for integration e.g. the mariner element from Drosophila mauritiana appears to recognize specific nucleotide patterns as potential sites for integra- tion [24]. Conclusion A comprehensive genome analysis of the three complete sequences of P. falciparum, P. y. yoelii and P. vivax revealed that a decrease in the frequency of transposable elements coincides with an increase in AT bias. A causal relation- ship between these two parameters remains to be estab- lished since there are limitations in the currently available bioinformatic screening methods. However, the hypothe- sis that a genoprotective mechanism exists in P. falciparum and that this may contribute to the compositional bias should be considered. Whole genome analytical methods that are particularly suited to compositionally biased genomes would be of value in further understanding the P. falciparum genome. Methods Protein databases Protein sequences, as opposed to nucleic acid sequences, were used as they tend to be more sensitive and specific and the signature domains used in this study are all pro- tein coding. Protein domain signatures characteristic of MGEs and their derivatives were identified based on their annotation in InterPro (release 12) [15] and Pfam-A (ver- sion 19) [16] databases and for which supportive evi- dence could be found in the literature. MGE signature domains that are present in host proteins were considered potential domesticated derivatives and were included in this study e.g. telomerase is a domesticated derivative of non-LTR retrotransposons and contains the signature domain of a reverse transcriptase (RT) [25]. The keywords used covered all potential known domains in MGEs as well as different classes of MGEs. InterPro and Pfam entries that did not yield any relationship to known MGEs or to domesticated were excluded. The keywords used were as follows: (i) for signature domains : transposase, reverse tran- scriptase, ribonuclease, integrase, protease, endonuclease, zinc finger, GAG polyprotein, maturase and recombinase. (ii) for classes of MGEs: transposon, retroelement, retrovi- rus, non-LTR retrotransposon, LTR retrotransposon and group II introns. HMM for group II introns The signature domains of group II introns are not well represented in InterPro or Pfam. Hidden Markov models (HMMs) were therefore generated for mitochondrial and chloroplast forms of this MGE (see [26] for original devel- opment of HMMs and [27] for a review of HMMs). The full lengths of individual group II introns were used to generate models as some of the signature domains (eg. domain X) were too short to generate any meaningful results. The 14 chloroplast and 19 mitochondrial group II introns used to build HMMs were as follows (accession numbers are those in GenBank): Chloroplast: X04826 (trnK I1), Z00044 (trnK I1), Z11741 (trnK I1), JN0302 (trnK I1), X52765 (trnK I1), X15901 (trnK I1), X57097 (trnK I1), D11467 (trnK I1), X04465 (trnK I1), P19593 (petD I1), X55877 (rbcL I1), X70810 (psbC I2, psbC I4 and psbD I8). Mitochondrial: X57968 (nad1 I4), M63034 (nad1 I4), M30176 (nad1 I4), M68929 (SrDNA I1, atp9 I1, atpA I1, atpA I2, cob I3, coxI I1, coxI I2, coxII I2), X14669 (coI I1), X55026 (COI I1, COI I4, ND5 I4), M62622 (cox1 I1, cox1 I2), X57546 (cox1 I1), X54421 (cob I1). The software package HMMER 2.3.2 [28] was used with default settings to generate HMMs. Only the P. falciparum organellar genomes were investigated. Reverse transcriptase domain The RT domain is common to all MGEs (including group II introns), except DNA transposons, and has been the most intensively studied MGE domain. However, the divergent and abundant nature of RT containing sequences makes it difficult to construct a meaningful HMM or consensus sequence for use in BLAST searches and alignments. Based on biochemical knowledge of the RT domain such as its crystal structure and point mutation data [29,30], we generated a RT consensus sequence. This complimented the detection of potential MGEs and these findings were validated by comparison with the results from the InterPro and Pfam databases. Six of the seven conserved regions common to most RTs were included, namely domains 1 and 2 (fingers) and domains A, B', C and D (palm). Domain E (thumb) was not included as it was not possible to generate a meaningful sequence using this method (for a review of RT domains in MGEs see [31]). An initial consensus sequence of the RT domain was gen- erated that was representative of RT-encoding MGE classes (retroviruses/LTR retrotransposons, non-LTR retrotrans- posons, and group II introns) and two related domesti- cated MGEs (a telomerase and a telomere associated non- LTR retrotransposon). The consensus sequence was gener- Page 8 of 10 (page number not for citation purposes)