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Figure 1 | BMC Bioinformatics

Figure 1

From: More robust detection of motifs in coexpressed genes by using phylogenetic information

Figure 1

Flowchart of our algorithm. Input data: Based on microarray data, coexpressed genes are identified. For each of these coexpressed genes, the orthologous intergenic sequences are identified. Step 1: BlockSampler: within a set of orthologous intergenic sequences, conserved blocks are detected and stored as a Position Specific Scoring Matrix (PSSM). Step 2: BlockAligner: The resulting PSSM's corresponding to conserved blocks, are aligned to each other with BlockAligner, which is a local alignment tool that assigns a p-value to each alignment as a quality measure. Step 3: based on all these pairwise comparisons and their corresponding p-values, a clustering is performed to group intergenic regions with a similar regulatory motif. Based on the BlockAligner results, a regulatory motif model is constructed for each cluster. Step 4: the detected motif models are used to screen all intergenic regions that were the input for the methodology.

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