detectIR

detectIR detects perfect and imperfect inverted repeats in genomic sequences to identify secondary DNA structures such as hairpins and cruciforms that are relevant to diverse biological processes.

Key Features:

• Implementation: Implemented in MATLAB.
• Algorithm: Transforms conventional sequence string comparison into vector calculations of complex numbers.
• Imperfect inverted repeat detection: Accommodates mismatches within the pairing stem to identify imperfect inverted repeats.
• Non-palindromic spacer handling: Allows for non-palindromic spacers (loops or gaps) in the middle of inverted repeats.
• Scalability: Capable of processing genome-scale sequence inputs.
• Comparative performance: Demonstrated higher speed and precision in comparative analyses, identifying inverted repeats missed by existing tools in sequences from HIV-1, Arabidopsis thaliana, Homo sapiens, and Zea mays.

Scientific Applications:

• Secondary structure identification: Detection of sequence motifs that form hairpins and cruciforms for studies of DNA secondary structure.
• Genomic repeat analysis: Analysis of inverted repeats across prokaryotic and eukaryotic genomes.
• Comparative genomics: Comparative detection of inverted repeats in viral, plant, and animal genomes including HIV-1, Arabidopsis thaliana, Homo sapiens, and Zea mays.
• Study of biological processes: Investigation of the roles of inverted repeats and associated secondary structures in genomic function and regulation.

Methodology:

Implemented in MATLAB using an algorithm that converts sequence string comparisons into vector calculations of complex numbers and permits mismatches in stems and non-palindromic spacers.