SeLOX

SeLOX identifies degenerate lox-like sites in genomic sequences to support site-specific recombinase-based genome engineering such as Cre recombinase-mediated excision of integrated retroviruses.

Key Features:

• Degenerate lox-like site detection: Searches for two inverted repeats flanking a variable-length spacer characteristic of lox-like recombination sites.
• Position weight matrix scoring: Calculates a position weight matrix based on known lox-like sequences to score candidate sites.
• Binary sequence transformation: Converts sequences into binary space to enable efficient encoding of nucleotide patterns.
• Bit-wise Boolean comparisons: Uses bit-wise AND operations on binary-encoded sequences for rapid and accurate matching.
• Large-scale genome searches: Applies the search approach to large genomic datasets, including whole-genome scans.

Scientific Applications:

• Cre-mediated retrovirus excision (HIV-1 LTR): Identification of lox-like sites suitable for Cre recombinase excision of integrated HIV-1 proviral long terminal repeats (LTRs).
• Yeast recombinase target discovery: Detection of lox-like sites compatible with six different yeast recombinases.
• Human genome screening: Genome-wide search for Cre-type recombination sites across the human genome.
• Site-specific recombination engineering: Supports selection of target sites for site-specific recombinase applications in genome engineering experiments.

Methodology:

SeLOX computes a position weight matrix from known lox-like sequences, converts target sequences into binary representations, and employs bit-wise AND Boolean comparisons to locate inverted repeats flanking variable-length spacers.