iFORM

iFORM (incorporating Find Occurrence of Regulatory Motifs) is a software tool to accurately identify transcription factor (TF) binding sites in DNA sequences. Using Fisher's combined probability test, the tool utilizes position weight matrices (PWMs) to describe TF motifs and integrates five classical motif discovery programs. This integration enables iFORM to achieve higher accuracy and sensitivity than individual motif discovery methods, as demonstrated by performance assessments using receiver operating characteristic (ROC) curves and correlation-based approaches. iFORM has been successfully applied to various datasets from the ENCODE Project and the NIH Roadmap Epigenomics Project, providing valuable insights into the roles of functional elements in transcriptional regulation.