chips

chips calculates the Nc codon usage statistic from coding nucleotide sequences to quantify codon usage bias for studies of gene expression and molecular evolution.

Key Features:

• Nc calculation: Calculates the effective number of codons (Nc) for coding sequences to quantify codon usage bias.
• Nucleotide sequence analysis: Analyzes coding nucleotide sequences to derive codon usage metrics.
• EMBOSS integration: Operates within the EMBOSS environment and leverages EMBOSS C libraries for sequence processing.
• Customization and extensibility: Supports modification and extension via EMBOSS C programming libraries and ACD file development.

Scientific Applications:

• Gene expression inference: Use codon usage metrics to help identify putatively highly expressed genes.
• Selection analysis: Infer selective pressures on genes by quantifying codon usage bias.
• Evolutionary studies: Study molecular evolution and codon usage patterns across genes and genomes.
• Comparative genomics: Compare codon usage across organisms to explore genetic adaptations.

Methodology:

Computes the effective number of codons (Nc) from coding nucleotide sequences to quantify codon usage bias.