PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction.

ABSTRACT:

Background

The specific recognition of a DNA locus by a given transcription factor is a widely studied issue. It is generally agreed that the recognition can be influenced not only by the binding motif but by the larger context of the binding site. In this work, we present a novel heuristic algorithm that can reconstruct the unique binding sites captured in a sequencing experiment without using the reference genome.

Results

We present PAPerFly, the Partial Assembly-based Peak Finder, a tool for the binding site and binding context reconstruction from the sequencing data without any prior knowledge. This tool operates without the need to know the reference genome of the respective organism. We employ algorithmic approaches that are used during genome assembly. The proposed al

SUBMITTER: Faltejskova K 

PROVIDER: S-EPMC10731698 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature