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Figure 1 | BMC Genomics

Figure 1

From: Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum

Figure 1

Sequence logos for the G-rich motif-sets given in Table 2 and identified in the upstream regions of the set of 22 transcription machinery genes. The logos have been manually aligned so that equivalent nucleotide positions, in the motif-sets used to generate them, lie approximately one below the other. The caption for each logo indicates the program that identified the motif-set, the group of genes whose upstream regions are being considered, the consensus motif for the motif-set and information about the motif-set output by the program. For the AlignACE logos, the caption gives the MAP (maximum a priori log likelihood [25]), group specificity and positional specificity scores, the preferred position at which the motifs occur and the number of motif occurrences in the set of upstream regions. For the Weeder logo, the caption gives a significance score, the number of 'redundant' consensus motifs related to the given one and the number of motif occurrences in the set of upstream regions when 1 mutation and a match percentage ≥ 90% are allowed. For the MEME logo, the caption gives the mode in which the program has been run, the width of the motif, the number of motif occurrences or sites in the set of upstream regions, the log likelihood ratio and the expectation value. Similar information is provided for the logos in Figures 2, 3 and 4.

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