GRASP

GRASP improves homology detection and gene annotation in metagenomic datasets by simultaneously searching and assembling overlapping database sequences guided by reference proteins to recover homologs of fragmented short-peptides derived from next-generation sequencing (NGS) reads or assembled nucleotide contigs.

Key Features:

• Simultaneous search-and-assemble algorithm: A novel algorithm that concurrently searches for and assembles overlapping database sequences guided by a reference sequence.
• Fragmented short-peptide handling: Targets partial-length proteins and short-peptides typical of NGS reads and assembled nucleotide contigs to improve homology detection.
• Improved sensitivity with maintained specificity: Demonstrates higher sensitivity than BLASTP, PSI-BLAST, and FASTM while retaining high specificity.
• Empirical evaluation: Performance validated using both simulated and real datasets.
• Quantitative metagenomic outputs: Facilitates detection and quantification of taxonomic and protein family abundances in complex metagenomic datasets.
• Implementation: Implemented in GNU C++.

Scientific Applications:

• Metagenomic gene annotation: Improves annotation accuracy for partial-length protein sequences in metagenomic studies.
• Homolog detection in fragmented databases: Identifies homologs of reference protein sequences within databases containing incomplete metagenomic proteins.
• Taxonomic and protein family profiling: Supports detection and quantification of taxonomic groups and protein family abundances from fragmented sequence data.

Methodology:

Uses a novel algorithm that simultaneously searches and assembles overlapping database sequences guided by a reference sequence; evaluated by comparison to BLASTP, PSI-BLAST, and FASTM on simulated and real datasets; implemented in GNU C++.