Reliable 16S rDNA

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Reliable 16S rDNA

In this context, a reliable, or error-free, 16S rDNA sequence, is one which lacks any obvious methodological artifact and is therefore, as far as can be ascertained, an accurate representation of the original DNA template from which it was constructed.

Programs such as Pintail and Mallard attempt to recognise and characterise anomalous sequences by a comparative analysis with reliable sequences.

How to recognise a reliable sequence?

Based on our current imperfect knowledge of the 16S rRNA gene, the only certain way of determining whether or not a newly sequenced 16S rDNA sequence is reliable is to compare it with a reliable 16S rDNA sequence.

A circular argument? Not really, since the vast amount of 16S rDNA sequence information now available to researchers, generated with different methods by different research groups, means that under most circumstances, a single sequence can now be compared with numerous independently produced records before a settled judgment is reached.

However, the circularity of this statement does highlight the limitation of any comparative analysis when checking for sequence errors; such analyses are only as reliable as the sequences available for comparison. Bacterial phylogenetic groups are not equally represented in the public sequence repositories, and so sometimes, with current techniques, it is just not possible to conclude whether or not a particular sequence is free from error.

Pintail and Mallard, in common with all other currently available methods for detecting anomalies, are ultimately limited by the quality, size, and range of the the public sequence repositories, and this needs to be borne in mind whenever any such analysis is undertaken.