NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes

By Todd Z. DeSantis, Philip Hugenholtz, Keith Keller, Eoin L. Brodie, Neil Larsen, Y. Piceno, R. Phan, Gary L. Andersen. Nucleic Acids Res., 2006

1,061 citations recorded by the source corpus.

Microbiologists conducting surveys of bacterial and archaeal diversity often require comparative alignments of thousands of 16S rRNA genes collected from a sample. The computational resources and bioinformatics expertise required to construct such an alignment has inhibited high-throughput analysis. It was hypothesized that an online tool could be developed to efficiently align thousands of 16S rRNA genes via the NAST (Nearest Alignment Space Termination) algorithm for creating multiple sequence alignments (MSA). The tool was implemented with a web-interface at . Each user-submitted sequence is compared with Greengenes' ‘Core Set’, comprising ∼10 000 aligned non-chimeric sequences representative of the currently recognized diversity among bacteria and archaea. User sequences are oriented and paired with their closest match in the Core Set to serve as a template for inserting gap characters. Non-16S data (sequence from vector or surrounding genomic regions) are conveniently removed in the returned alignment. From the resulting MSA, distance matrices can be calculated for diversity estimates and organisms can be classified by taxonomy. The ability to align and categorize large sequence sets using a simple interface has enabled researchers with various experience levels to obtain bacterial and archaeal community profiles.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/31fcf5dc64a4fc5ca367b48b150acde918680498

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology

In Molecular Biology

Citations in the corpus

The influence of sex, handedness, and washing on the diversity of hand surface bacteria (2008, methodology): “DeSantis T, et al. (2006) NAST: A multiple sequence alignment server for comparative analysis of 16S rRNA genes.”
Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice (2010, methodology): “The usable V3 unique sequences were aligned using NAST (DeSantis et al., 2006), and then imported into the ARB (Ludwig et al., 2004) to construct a neighbour-joining tree for online UniFrac analysis (Lozupone et al., 2006).”
Shifts in bacterial community structure associated with inputs of low molecular weight carbon compounds to soil (2010, methodology): “The set of all representative sequences were aligned through NAST (DeSantis et al., 2006) using a minimum alignment length of 190 nt and sequence identity of 70% as parameters and with lanemask PH to screen out hypervariable regions of sequences (http://greengenes.”
Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies (2011, methodology): “Identification of chimeras and sequencing errors All reference and de novo sequences were aligned to a 50,000column wide SILVA-based reference alignment using mothur’s NAST-based aligner [39,40].”
Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine (2009, neutral): “These methods included i) selecting the most common classification from the best BLAST [31] hits against reference sequences from the RDP database; ii) the online RDPclassifier with bootstrap values$50% (see further below); iii) the online Greengenes classifier [32] based on NAST alignments [33]; iv”
Evolution of Symbiotic Bacteria in the Distal Human Intestine (2007, methodology): “Phylogenetic trees were constructed based on alignment of 16S rRNA fragments using the NAST aligner [53].”
Soil carbon content drives the biogeographical distribution of fungal communities in the black soil zone of northeast China (2015, methodology): “A representative sequence from each phylotype was aligned using the Python Nearest Alignment Space Termination (PyNAST) tool (DeSantis et al., 2006; Caporaso et al., 2010) with a relaxed neighbor-joining tree built using FastTree (Price et al.”
A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses (2009, methodology): “DNA sequences from the clone libraries were aligned using the NAST aligner (DeSantis et al., 2006).”
Evidence for a core gut microbiota in the zebrafish (2011, methodology): “Contiguous sequences with at least 700 bp 4Q20 were aligned using the NAST server (DeSantis et al., 2006), and putative chimeras were identified and excluded using Bellerophon version 3 implemented at the Greengenes website (http://greengenes.lbl. gov; match length to core set sequence threshold of…”
PyNAST: a flexible tool for aligning sequences to a template alignment (2009, methodology): “[10:29 7/1/2010 Bioinformatics-btp636.tex] Page: 266 266–267 Motivation: The Nearest Alignment Space Termination (NAST) tool is commonly used in sequence-based microbial ecology community analysis, but due to the limited portability of the original implementation, it has not been as widely adopted…”