Question: Features that distinguish phyla in 16S sequences
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gravatar for grp2009
3.5 years ago by
grp200940
grp200940 wrote:

Is there a way to use RDP (Ribosomal Database Project) or a similar taxonomy classification tool to produce localized "features" that distinguish 16S sequences based on their phyla? By "feature" I mean something like a region of the 16S sequence that is particularly important in distinguishing between two taxa.

Background: I am comparing different pipelines for the analysis of bacterial 16S sequences. In some cases I see that different read preparation strategies (for example, truncating reads differently) lead to clear changes in the relative abundance of taxa (at the phylum level, for example). I am trying to trace this issue to its cause, and thought that it might help to know which regions of the 16S are especially important in distinguishing two given taxa.

sequencing next-gen • 711 views
ADD COMMENTlink modified 3.5 years ago by lakhujanivijay5.0k • written 3.5 years ago by grp200940
1
gravatar for lakhujanivijay
3.5 years ago by
lakhujanivijay5.0k
India
lakhujanivijay5.0k wrote:

Variable regions of 16S rRNA are frequently used in phylogenetic classifications at different taxonomic levels in diverse sets of microbial populations. Which variable region(s) to sequence is an area of debate and your region(s) of interest might vary depending on your objectives, experiment design, and sample type etc. Generally, V3 and V4 regions of the 16S rRNA gene are used as "feature".

Check out these links:

http://www.nature.com/nrmicro/journal/v12/n9/fig_tab/nrmicro3330_F1.html

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2562909/

http://www.sciencedirect.com/science/article/pii/S0167701210002745

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by lakhujanivijay5.0k
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