GPress

GPress compresses and enables fast querying of General Feature Format (GFF), GTF, and GFF3 genomic annotation files and linked expression files to reduce storage footprint while preserving annotations that represent features in DNA, RNA, and protein sequences and supporting identifier- and coordinate-based retrieval.

Key Features:

• Supported formats: Handles General Feature Format (GFF), GTF, GFF3 annotation files and linked feature expression files.
• Compressed querying: Performs queries directly on compressed data to reduce storage footprint without compromising retrieval accuracy.
• Integration with expression files: Compresses and queries expression/feature expression files alongside genomic annotations.
• High compression efficiency: Achieves average size reductions of approximately 98% for GFF files and greater than 92% for linked expression files.
• Fast retrieval times: Retrieves all annotations for a unique identifier from a human GFF in ~2.47 seconds and items within a coordinate range in ~4.61 seconds.
• Query types: Supports identifier-based and genomic coordinate-range queries without full decompression of datasets.
• Data integrity: Preserves annotation integrity during compression and storage.

Scientific Applications:

• Genomic annotation management: Efficient storage and retrieval of large annotation datasets for diverse organisms.
• Integration with expression analysis: Combined handling of annotation and expression files to streamline gene expression studies.
• Large-scale sequencing projects: Reduces storage needs and accelerates access to annotations in high-throughput sequencing workflows.
• Coordinate- and identifier-based queries: Rapid extraction of features for downstream analyses requiring region- or ID-specific annotation retrieval.

Methodology:

Employs advanced compression algorithms tailored for GFF and expression files and a querying mechanism optimized for speed that allows precise searches based on identifiers or genomic coordinates without decompressing entire datasets.