Pat Schloss on rRNA Reference Database Sequence Alignment · Kylepedia

Pat Schloss on rRNA Reference Database Sequence Alignment

Source Information

Source: Mothur blog

PD Schloss

Aug 4, 2015



This blog post suggests some food for thought for the alignment of rRNA reference databases. Pat Schloss is pretty candid here, and provides some strong arguments in favour of using a “reference-based” alignment approach, rather than approaches that model the secondary structure of the 16S rRNA gene.



Dr. Schloss’ results indicate that the model-based approaches result in the loss of a significant # of bases in the hypervariable regions. For example, the Greengenes alignments resulted in 18 sequences being discarded on average compared to SILVA’s. This surprised me, as I was under the impression that Infernal was the goto tool for rRNA alignments. This post could also prove to be helpful in the future, when we perform alignments on our database, as the source code is provided.