Silva reference files

From mothur

Release 119

The SILVA alignment is 50,000 columns long so that it can be compatible with 18S rRNA sequences as well as archaeal 16S rRNA sequences. The actual reference alignment that SILVA uses with their SINA aligner is called the SEED alignment. We don't know what this actually is. We have tried to duplicate it by identifying the unique sequences in the SSURef database that have a 100% alignment score to the SEED alignment. For the Bacteria we require that the sequences be full length going from the end of the traditional 8f/27f primer to the beginning of the traditional 1492r primer. For the Archaea and Eukarya we require that they be longer than 900 bp. We are providing separate datasets for bacterial, archaeal, and eukaryotic sequences. Within each reference set are the aligned sequence file (e.g. silva.bacteria.fasta), an unaligned sequence file (e.g. nogap.bacteria.fasta), and the silva taxonomy outline (e.g. There is a README in each that gives the exact commands for how the references were created:

Release 102

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