SEDA

SEDA processes FASTA files containing DNA and protein sequences to prepare and transform sequence datasets for downstream phylogenetic and selection analyses.

Key Features:

• FASTA processing: Processes FASTA files containing DNA and protein sequences for dataset preparation.
• Data transformation protocols: Transforms genome datasets into formats suitable for downstream analyses.
• Remove isoforms operation: Removes coding-sequence isoforms to accelerate generation of sequence data files for phylogenetic analyses.

Scientific Applications:

• Gene evolution studies: Enables analysis of comprehensive genome datasets beyond model species, exemplified by investigation of the GULO gene across Protostomian groups (Molluscs, Priapulida, Arachnida) revealing putative functional genes.
• Positive selection analysis: Supports identification of positively selected amino-acid sites within gene families, demonstrated for primate HLA immunity genes where MHC class I and II show significant positive selection alongside purifying selection.

Methodology:

Operations explicitly include the "Remove isoforms" operation and transformations of FASTA DNA/protein datasets into formats suitable for downstream phylogenetic and selection analyses.