Work

GenoCLAMP: consolidation of sequence motifs from genomic-scale data

Year: 2026

Type: article

Abstract: Genome-wide protein–DNA mapping studies have produced thousands of enriched sequence motifs, many of which are redundant because transcription factors (TFs) bind cooperatively as distinct complexes to shared sites. Here, we present Genomic CLustered Alignment of Motif Profiles (GenoCLAMP), an algorithm that unifies motif-clustering and alignment to collapse redundant motifs into high-quality merged matrix representations. We demonstrate that GenoCLAMP reliably recovers known TF complexes that bind common motifs and uncovers evidence for previously uncharacterized motifs. These results establish GenoCLAMP as a robust and efficient framework for motif consolidation, enhancing computational analyses and biological interpretation of large-scale TF–DNA binding datasets.

Source: Genome biology

DOI: 10.1186/s13059-026-04283-9

Authors: Justin Sungsoo Cha, B. Franklin Pugh, William K. M. Lai

Institutions: Cornell University, University at Buffalo, State University of New York

Language: English

Topic: Genomics and Chromatin Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $5,490

OpenAlex ID: W7222752043

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