MitoBank

MitoBank retrieves and parses mitochondrial genomes from GenBank to extract and store individual mitochondrial genes for downstream evolutionary and model-selection analyses of metazoan mitochondrial proteins.

Key Features:

• GenBank retrieval: Retrieves mitochondrial genome records from GenBank.
• Parsing and gene extraction: Parses GenBank records and extracts individual mitochondrial genes into separate files.
• Gene type support: Extracts both coding and RNA genes and provides sequences in amino acid or nucleotide form.
• File storage: Stores each extracted gene in its own output file for downstream analysis.
• Implementation: Implemented as a Perl script.
• Model-evaluation support: Facilitates statistical evaluation of substitution models for mitochondrial proteins, including consideration of matrices such as MtREV and MtMam and gene-specific behavior (e.g., Nd6).
• Taxon-specific model construction: Supports development and evaluation of taxon-specific matrices, exemplified by the MtArt matrix derived from arthropod mitochondrial proteomes.
• Metazoan scope: Enables analyses across metazoan taxonomic levels to investigate biases and variations in mitochondrial genetic codes.

Scientific Applications:

• Evolutionary analysis: Studying mitochondrial protein evolution across different metazoan taxonomic levels.
• Model selection: Determining best-fit substitution models for mitochondrial proteins.
• Substitution-matrix development: Constructing and validating taxon-specific substitution matrices such as MtArt for arthropods.
• Comparative genomics: Comparing biases and variations in mitochondrial genetic codes and gene-specific behavior (e.g., Nd6) across taxa.

Methodology:

Implemented as a Perl script that retrieves mitochondrial genomes from GenBank, parses records to extract individual coding and RNA genes, stores each gene in separate files and outputs sequences as nucleotide or amino-acid sequences; used with statistical model-selection approaches to evaluate substitution matrices (e.g., MtREV, MtMam, MtArt) and to construct matrices such as MtArt from arthropod mitochondrial proteomes.