SELEX

SELEX quantifies DNA binding specificities from SELEX-seq (Systematic Evolution of Ligands by Exponential Enrichment) sequencing data to characterize protein–DNA interactions.

Key Features:

• Integration with Bioconductor: Implements analysis within the Bioconductor ecosystem to enable interoperability with other Bioconductor packages and workflows.
• R-based statistical processing: Performs statistical processing of SELEX-seq datasets using the R programming language.
• Interoperable package ecosystem: Operates as part of a suite of 934 interoperable Bioconductor packages contributed by the scientific community.
• Formal review and automated testing: Packages undergo formal initial review and continuous automated testing to promote software reliability.

Scientific Applications:

• Quantification of binding specificities: Quantifies DNA binding specificities from SELEX-seq data to infer protein sequence preferences.
• Identification of binding motifs: Identifies preferred DNA sequences and enriched motifs bound by proteins from SELEX-seq enrichment profiles.

Methodology:

Computational analysis of SELEX-seq data using R for statistical processing of DNA–protein interaction signals.