ANACONDA

ANACONDA analyzes gene primary structures to characterize codon usage, codon context, nucleotide repeats, and codon expansions for genomic-scale sequence feature analysis.

Key Features:

• Codon analysis: Investigates codon bias and codon context across genomes to assess preferential codon usage and local contextual dependencies.
• Statistical methods: Implements contingency table analysis, residual analysis, and multivariate analysis including cluster analysis to quantify associations and clustering of codons.
• Visualization techniques: Generates visual representations of codon usage patterns and other sequence features for comparative and global analyses.
• Nucleotide repeats analysis: Identifies nucleotide repeats within open reading frames (ORFeome) to characterize repetitive sequence elements.
• Codon expansion detection: Detects genes with expanded codons, often resulting from DNA replication errors, to flag candidates potentially linked to human diseases.

Scientific Applications:

• Genomic research: Provides a global view of sequence features and codon usage applicable to genomes such as Saccharomyces cerevisiae, Candida albicans, and Escherichia coli.
• Disease research: Identifies genes with expanded codons to support discovery of genes associated with human diseases.

Methodology:

Downloads gene sequences from public databases in FASTA and GenBank formats and applies statistical analyses and visualization methods to analyze sequences at genomic scale.