Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation.

ABSTRACT: Core promoters are stretches of DNA at the beginning of genes that contain information that facilitates the binding of transcription initiation complexes. Different functional subsets of genes have core promoters with distinct architectures and characteristic motifs. Some of these motifs inform the selection of transcription start sites (TSS). By discovering motifs with fixed distances from known TSS positions, we could in principle classify promoters into different functional groups. Due to the variability and overlap of architectures, promoter classification is a difficult task that requires new approaches. In this study, we present a new method based on non-negative matrix factorisation (NMF) and the associated software called seqArchR that clusters promoter sequences based on their mot

SUBMITTER: Nikumbh S 

PROVIDER: S-EPMC10695386 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature