Align sequences


Given a fasta file of 16S rRNA sequences, aligns them to the Silva 16S rRNA reference alignment template. You can use either the Silva reference or provide your own reference alignment in fasta format. When using the Silva reference you should be aware of their dual-use license: Silva is free for academic users, but commercial users need to purchase a license.



Sequences in are aligned, one by one, against the Silva 16S rRNA reference set. Kmer searching with 8mers is followed by Needleman-Wunsch pairwise alignment. Please indicate the region of the reference alignment that your amplified region corresponds to, as this will improve the overall alignment quality and save space. For example, for the V4 region of the 16S rRNA gene in bacteria you can set Start = 13 862 and End = 23 444.

The alignment result is given in fasta format, with periods ('.') leading up to the first base in the sequence and following the last base of the sequence.

The speed of this tool depends on the number and length of your sequences, and the number and length of the sequences in the reference template.

This tool is based on the Align.seqs and Pcr.seqs commands of the Mothur package.


The analysis output consists of the following:


Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.