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| Near Neighbors & Type Strains |
What is a near neighbor or named isolate?
Greengenes offers the user an opportunity to have
near-neighbors returned along with the submitted sequences when doing
alignment. This can be useful to have in your FASTA file as you
proceed with classification and making a tree. Near-neighbors are
just that, other bacteria that have a very similar 16S sequence. They
give the user an idea of how close what they have classified is to
other previously identified organisms.
Named isolates are similar to near-neighbors but are
more specific. A named isolate is a bacteria that may not be the
most closely related strain to your submitted sequence but gives you a
landmark by which to get an idea of what it is that you have.
The named isolate is frequently the first organism in that
taxonomic
grouping to have been described in the academic literature. All
others
that follow in that same group are compared to the named isolate.
In general, named isolates are defined by the following:
- An organism that has been cultured in a laboratory environment
- Is available by mail order from a culture collection
- Has been phenotypically described in the academic literature
Trees
Alignment
Greengenes Main |
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