[Taxacom] Is this the future?

David Campbell pleuronaia at gmail.com
Fri Jul 19 06:52:34 CDT 2013

> Genbank: it is not up to the task of matching taxa. Little taxonomic
> coverage, many misidentifications, hardly at a stage where you can throw a
> sequence and get a generic ID (forget specific).

A big problem is that it is at a stage where anyone can throw in a sequence
and get a generic or specific ID; however, the chances of that ID actually
being correct are often quite poor, especially in diverse, understudied
groups.  Of course, that is what the the original post meant, but I am
highlighting the fact that many databases, including GenBank, can readily
be used to give a false confidence in results.

Another significant problem is the increasing number of known instances
where the barcode gives misleading or incorrect results.  Nuclear copies,
divergent alleles of unknown origin, bacterial genes, nontarget eukaryotic
genes, bad data....   The universality of primers necessary for large-scale
environmental genomics surveys necessitates both that they will readily
amplify a number of non-target sequences and that they won't be optimized
for all target sequences.  And unless you actually know something about the
organism it came from and examine the results, you won't notice that
there's something wrong.  Phylogenetic programs will process whatever
sequences you input, and too often unexpected results are clear proof that
all previous analyses were wrong rather than a reason to question one's own

Dr. David Campbell
Assistant Professor, Geology
Department of Natural Sciences
Gardner-Webb University
Boiling Springs NC 28017

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