A Final Attempt at Finding DnaA Boxes in E. coli
Discover how to identify DnaA box sequences in the E coli genome by analyzing frequent 9-mers with mismatches and reverse complements around the minimum skew position. Understand the challenges of pinpointing replication origins using bioinformatics and the importance of collaboration with biologists for verifying computational predictions.
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We now make a final attempt to find DnaA boxes in E. coli by finding the most frequent 9-mers with mismatches and reverse complements in the region suggested by the minimum skew as ori. Although the minimum of the skew diagram for E. coli is found at position 3923620, we shouldn’t assume that its ori is found exactly at this position due to random fluctuations in the skew. To remedy this issue, we could choose a larger window size (e.g., ...