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Align.seqs (version

Mothur Overview

Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki.

Command Documentation

The align.seqs command aligns a user-supplied fasta-formatted fasta sequence file to a user-supplied fasta-formatted template_alignment.

The general approach is to
  1. find the closest template for each fasta using kmer searching, blastn, or suffix tree searching;
  2. to make a pairwise alignment between the fasta and de-gapped template sequences using the Needleman-Wunsch, Gotoh,or blastn algorithms; and
  3. to re-insert gaps to the fasta and template pairwise alignments using the NAST algorithm so that the fasta sequence alignment is compatible with the original template alignment.

In general the alignment is very fast - we are able to align over 186,000 full-length sequences to the SILVA alignment in less than 3 hrs with a quality as good as the SINA aligner. Furthermore, this rate can be accelerated using multiple processors. While the aligner doesn't explicitly take into account the secondary structure of the 16S rRNA gene, if the template database is based on the secondary structure, then the resulting alignment will at least be implicitly based on the secondary structure.