BACKGROUND: To date, only a few transcription factors have been identified in 
the genome of the parasite Plasmodium falciparum, the causative agent of 
malaria. Moreover, no detailed molecular analysis of its basal transcription 
machinery, which is otherwise well-conserved in the crown group of eukaryotes, 
has yet been reported. In this study, we have used a combination of sensitive 
sequence analysis methods to predict the existence of several parasite encoded 
general transcription factors associated with RNA polymerase II.
RESULTS: Several orthologs of general transcription factors associated with RNA 
polymerase II can be predicted among the hypothetical proteins of the P. 
falciparum genome using the two-dimensional Hydrophobic Cluster Analysis (HCA) 
together with profile-based search methods (PSI-BLAST). These predicted 
orthologous genes encoding putative transcription factors include the large 
subunit of TFIIA and two candidates for its small subunit, the TFIIE 
beta-subunit, which would associate with the previously known TFIIE 
alpha-subunit, the TFIIF beta-subunit, as well as the p62/TFB1 subunit of the 
TFIIH core. Within TFIID, the putative orthologs of TAF1, TAF2, TAF7 and TAF10 
were also predicted. However, no candidates for TAFs with classical histone fold 
domain (HFD) were found, suggesting an unusual architecture of TFIID complex of 
RNA polymerase II in the parasite.
CONCLUSION: Taken together, these results suggest that more general 
transcription factors may be present in the P. falciparum proteome than 
initially thought. The prediction of these orthologous general transcription 
factors opens the way for further studies dealing with transcriptional 
regulation in P. falciparum. These alternative and sensitive sequence analysis 
methods can help to identify candidates for other transcriptional regulatory 
factors in P. falciparum. They will also facilitate the prediction of biological 
functions for several orphan proteins from other apicomplexan parasites such as 
Toxoplasma gondii, Cryptosporidium parvum and Eimeria.