FeatureScan

FeatureScan identifies novel DNA sequence similarities by comparing physico-chemical properties of DNA double strands using a signal theory-based approach to reveal information not captured by letter-based similarity measures.

Key Features:

• Physico-Chemical Property Analysis: Evaluates DNA parameters including charge, melting enthalpy, and conformational parameters to detect sequence similarities.
• Signal Theory-Based Approach: Applies signal theory instead of letter-based measures to uncover hidden information within DNA primary structure.
• Comprehensive Parameter Set: Employs thirty-eight distinct physico-chemical properties for analysis.
• Output Formats and Database Links: Reports matches in FASTA format and links results to ENSEMBL, NCBI, and UCSC.
• FFT Acceleration: Uses specialized hardware for fast Fourier transformations to enable rapid, genome-scale analysis.

Scientific Applications:

• Promoter analysis in E. coli: Applied to promoters of E. coli genes, detecting similarities that correlate with transcriptional regulatory responsiveness under antibiotic and osmotic treatments.
• Gene regulation studies: Supports genomic research into gene regulation mechanisms by identifying physico-chemical similarity relationships among sequences.

Methodology:

Comparison of DNA double-strand physico-chemical parameters using a signal theory-based analysis of primary sequence properties, with computations accelerated by specialized hardware for fast Fourier transformations to enable rapid analysis of entire eukaryotic genomes.