Figure 1

Repeated FIRE searches of 5′ gene flanking regions in P. falciparum . (A) Schematic representation of sequences used for the repeated FIRE analysis. The relative position of three hypothetical head-to-head orientated genes (pentagonal arrows) are illustrated with a scale for the intergenic distance (bp) shown above. In groups A and C, up to 1000 bp of intergenic sequence from either the start of the right-hand gene (group A) or from a position 500 bp upstream of the gene (group C) are secured. Where this 1000 bp window overlaps with the flanking left-hand gene, the sequences are truncated at the start of that gene. For groups B and D, the position of the window is the same as groups A and C, respectively. In this case only when all 1000 bp of sequence can be captured is this done. In this way, different, but related input sequence files can be subjected to a FIRE search. (B) Examples of FIRE motif heat-map output. The colour map illustrates over-representation (yellow) and under-representation (blue) of discovered DNA motifs in 5′ flanking regions of genes that share the same temporal profile of mRNA accumulation during intraerythrocytic development. The approximate morphological staging of these time points is illustrated above the colour map. To the right of the colour map the seed search sequence and the optimized motif (as a WebLogo) are shown along with qualitative and quantitative data reporting the score of the discovered motif, the reliability of the search and data relating to bias in position and orientation. These variables are explained in the main text. Full data for all groups are provided in Additional file 1.