GAST

GAST assigns taxonomy to small subunit ribosomal RNA (SSU rRNA) sequences by aligning query SSU hypervariable region tags to reference sequences to determine taxonomic composition of microbial communities.

Key Features:

• Taxonomic assignment: Aligns query SSU rRNA sequences to reference sequences and assigns taxonomy based on the consensus of nearest reference matches.
• Alignment distance reporting: Reports the alignment distance between query and reference sequences as a measure of similarity.
• Hypervariable region targeting: Uses hypervariable region tags instead of full-length SSU rRNA to enable deeper sampling depth.
• Massively parallel pyrosequencing compatibility: Supports processing of data generated by massively parallel pyrosequencing for extensive community sampling.
• Reduced cloning and chimera bias: Short-read strategy minimizes cloning bias and reduces chimera formation by sequencing hypervariable regions in single reads.
• Comparable taxonomy and abundance: Provides taxonomy and relative abundance measures comparable to those derived from full-length SSU rRNA sequences.
• Scalability for large projects: Enables rapid assessment of microbial community membership suitable for large-scale efforts such as the Human Microbiome Project.

Scientific Applications:

• Microbial community profiling: Determining composition and diversity of microbial communities across environments using SSU rRNA hypervariable regions.
• Human microbiome studies: Analyzing human gut microbiota and datasets from projects like the Human Microbiome Project.
• Environmental microbiology: Characterizing microbial communities in environments such as deep-sea hydrothermal vents.
• Rare biosphere investigation: Detecting members of the "rare biosphere" through deep sampling enabled by hypervariable region sequencing.

Methodology:

GAST aligns query SSU rRNA sequences to a comprehensive database of reference sequences, assigns taxonomy based on the consensus of nearest reference matches, and reports alignment distances as measures of similarity.