Identification of upstream transcription factor binding sites in orthologous genes using mixed Student's t-test statistics.

ABSTRACT:

Background

Transcription factor (TF) regulates the transcription of DNA to messenger RNA by binding to upstream sequence motifs. Identifying the locations of known motifs in whole genomes is computationally intensive.

Methodology/principal findings

This study presents a computational tool, named "Grit", for screening TF-binding sites (TFBS) by coordinating transcription factors to their promoter sequences in orthologous genes. This tool employs a newly developed mixed Student's t-test statistical method that detects high-scoring binding sites utilizing conservation information among species. The program performs sequence scanning at a rate of 3.2 Mbp/s on a quad-core Amazon server and has been benchmarked by the well-established ChIP-Seq datasets, putting Grit amongst the to

SUBMITTER: Huang T 

PROVIDER: S-EPMC9205514 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature