NAST

NAST aligns 16S rRNA gene sequences from bacteria and archaea to produce uniform multiple sequence alignments (prokaryotic MSAs or prokMSA) for comparative microbial taxonomy, phylogeny, and diversity analysis.

Key Features:

• Nearest Alignment Space Termination algorithm: efficiently aligns large numbers of 16S rRNA gene sequences and produces uniform prokaryotic MSAs (prokMSA).
• Uniform alignment output: generates standardized MSAs (prokMSA) to facilitate consistent comparative analyses across datasets.
• Core Set comparison: compares user sequences against the Greengenes 'Core Set' (~10,000 aligned non-chimeric sequences) and orients sequences by pairing them with closest matches to guide gap insertion.
• Data cleaning: automatically removes non-16S data, including vector sequences and flanking genomic regions, prior to alignment.
• Operational Taxonomic Units (OTUs): enables identification of OTUs from the prokMSA based on transitive sequence similarities.

Scientific Applications:

• Microbial diversity studies: supports surveys and community profiling of bacterial and archaeal diversity using aligned 16S rRNA sequences.
• Probe design: provides categorized 16S rDNA alignments to inform DNA probe design for taxonomic identification, demonstrated in studies categorizing organisms such as Staphylococcus aureus and Bacillus anthracis.
• Phylogenetic analysis: produces MSAs used to derive distance matrices for phylogenetic inference and estimation of microbial diversity.

Methodology:

Aligns user-submitted 16S rRNA gene sequences to a reference set (Greengenes Core Set), pairs sequences with closest matches to guide gap insertion, removes non-16S sequences (e.g., vector and flanking genomic regions), and constructs uniform prokaryotic MSAs using the Nearest Alignment Space Termination algorithm.