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. 2006 Jul 1;34(Web Server issue):W394-9.
doi: 10.1093/nar/gkl244.

"VSports app下载" NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes

T Z DeSantis Jr  1 , P Hugenholtz, K Keller, E L Brodie, N Larsen, Y M Piceno, R Phan, G L Andersen
Affiliations

NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes (VSports手机版)

T Z DeSantis Jr et al. Nucleic Acids Res. .

Abstract

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 http://greengenes. lbl. gov/NAST. Each user-submitted sequence is compared with Greengenes' 'Core Set', comprising approximately 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. VSports手机版.

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Figures

Figure 1
Figure 1
Locating a NAST alignment template for a user-supplied candidate sequence. Candidate sequence in green is matched to a near-neighbor aligned template in Greengenes' Core Set (grey) by tallying 7mers in common. The alignment ‘template’ is BLAST aligned to the candidate parameter q = −1 (favors long match). The candidate is then trimmed of flanking sequence data such as tRNA, intergenic spacer regions, vector sequence, 23S rDNA and sequence outside of the high-scoring pair (HSP) boundaries. If the HSP pairs opposite strands, then the candidate is reverse complemented.
Figure 2
Figure 2
Example of NAST compression of a BLAST pairwise alignment using a 38 character aligned template. Template and candidate is extended to 40 characters after (A) BLAST gap insertion and (B) retention of original template spacing. (C) Nucleotide insertions in the candidate relative to the template which force additional characters to be added in the template are identified at positions α and β. (D) A bi-directional search for the nearest alignment space (hyphen) relative to the insertion terminates at the positions indicated by the black arrows. The leftward search from the α position was shorter in distance compared with the rightward, thus the space to the left of ‘GT’ was removed. (E) The search from the β position encountered the alignment edge on the right, thus the position to the left of ‘AC’ was removed. (F) Lastly, the two template-extending spaces are deleted from the template. Notice that sequence data are not added to or overwritten in the candidate. The NAST removal of two characters from both sequences allowed local misalignments (underlined) while preserving the 38 character format of the global MSA.
Figure 3
Figure 3
Greengenes pre-processing and post-processing tools for use with the NAST aligner. ‘Trim’ can be used to remove poor quality DNA data before alignment. ‘Classify’ and ‘Distance’ receive NAST MSAs as input. ‘Export’ and ‘Download’ allow advanced users to append their MSA with select sequences from the public repositories.
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