From genome to expression hypotheses.
Inspect the evidence behind each prediction.
Which genes may turn on early—and why?
Analyze a genome to view its expression map, candidate regulatory sites, and the evidence supporting each gene’s phase.
The D29 example uses the same analysis engine as your own genome. No account or sequence database submission is needed by the analysis itself.
Research prototype. Regulatory motifs do not independently establish expression timing or DNA replication onset.
How Phagex uses regulatory and expression evidence
Phagex runs the original Python predictor with Biopython. It scans both DNA strands for the L5-like and Bxb1-like stoperator consensus models. A match is a candidate binding site, not evidence that a repressor is active. D29 studies also support promoter activity at some stoperator-associated sites.
Comparative phase assignments require both protein and upstream-sequence conservation with literature-derived L5 and Fruitloop (cluster F1) references. Functional annotations provide separate weak priors. These references describe broad regions from L5 induction and Fruitloop infection experiments, not precise gene-by-gene onset times. Distant phages may have many unresolved genes.
Measured expression uses a 20%-of-peak abundance threshold and your chosen early/late boundary. RNA/DNA normalization is a per-template abundance proxy; RNA stability remains a confounder. No raw RNA-seq processing, calibrated probabilities, or replication-origin prediction is included.