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Fig. 4 | Algorithms for Molecular Biology

Fig. 4

From: Regmex: a statistical tool for exploring motifs in ranked sequence lists from genomics experiments

Fig. 4

Regmex behavior in different scenarios, for 1000 sequences, each of length 1000 bases. a Comparison of p-value output for the different rank correlation methods used in Regmex. One 7-mer motif (ACGTGAT) is inserted as indicated in the first half of the sequences. In replicates with no insertion the BB method was used, but the other methods gave similar results. Error bars indicate standard error of 100 replicates. b Up to four different 7-mer motifs are inserted randomly in the first half of the sequences. p-value output from Regmex using the BB method is plotted against the number of inserted motifs. RE motifs define sets of one up to all four 7-mers as indicated, e.g., m1 | m2 = (ACGTGAT)|(GCATTGT). c Sets of four 7-mer motifs were inserted at fixed positions randomly among the first half of the sequences, so that motifs occur together in the same sequences. p-value output from Regmex using the BB method is plotted against the number of inserted motifs. RE motifs define sets of combinations of one up to all four 7-mers as indicated, e.g., m1 & m2 = (ACGTGATN*GCATTGT)|(GCATTGTN*ACGTGAT), where N denotes any nucleotide

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