CHAPAO

CHAPAO compresses multiple sequence alignments (MSAs) losslessly to reduce storage requirements and preserve information in biomolecular sequence datasets.

Key Features:

• Lossless MSA compression: Performs lossless compression of multiple sequence alignments (MSAs) for biomolecular data.
• Hierarchical referencing technique: Uses a hierarchical referencing scheme to represent redundancy across aligned sequences.
• Likelihood-based similarity analysis: Incorporates likelihood-based analyses of sequence similarities to guide referencing decisions.
• Graph-theoretic algorithms: Employs graph-theoretic algorithms as part of the compression strategy.
• Exploitation of sequence redundancy: Exploits inherent redundancy and special characteristics of biomolecular sequences to improve compression efficiency.
• Benchmark comparisons: Demonstrated compression gains relative to gzip, bzip2, 7-zip, MFCompress, and Nucleotide Archival Format (NAF).
• Target formats and data: Applicable to FASTA files and other biomolecular sequence data, including MSAs of 16S and 23S rRNA.
• Evaluated datasets: Evaluated on data from the avian phylogenomics project and the 1000 Plants project (1KP).

Scientific Applications:

• Storage of large-scale genomic alignments: Compresses MSAs from projects such as the avian phylogenomics project and the 1000 Plants project (1KP) for long-term storage.
• Archival of rRNA datasets: Reduces storage requirements for 16S and 23S rRNA sequence alignments.
• FASTA file archiving: Provides a compression option for FASTA-formatted biomolecular sequence datasets.
• Comparative benchmarking: Enables comparative evaluation of compression ratios against general-purpose and specialized compressors like gzip, bzip2, 7-zip, MFCompress, and NAF.

Methodology:

CHAPAO applies a hierarchical referencing technique that combines likelihood-based analyses of sequence similarities with graph-theoretic algorithms to perform lossless compression of MSAs.