Question: How can we find the 16S rRNA sequence of an organism from NCBI?
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gravatar for sinumolg
2.7 years ago by
sinumolg10
sinumolg10 wrote:

Hi All

I want to get the 16srRNA sequence of Staphylococcus aureus to do phylogeny along with other similar strains. Can anyone please help me to get the data? Is it available in NCBI or any other sources?

blast rna-seq next-gen gene genome • 1.6k views
ADD COMMENTlink modified 2.5 years ago by Charles Warden7.5k • written 2.7 years ago by sinumolg10
2

just search and filter from genbank.

ADD REPLYlink written 2.7 years ago by shenwei3565.0k

...I normally use Silva. Is Genbank better, in your opinion?

ADD REPLYlink written 2.6 years ago by Brian Bushnell17k
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gravatar for Charles Warden
2.5 years ago by
Charles Warden7.5k
Duarte, CA
Charles Warden7.5k wrote:

In most cases, it is difficult to confidently resolve classifications for 16S data at the species or sub-species level. So, if you were specifically interested in types of Staphylococcus aureus, it might be best to use a different marker (which you could define from comparing whole genome sequences from GenBank).

That said, there are a couple options to get relatively straight-forward taxonomy information for some reference 16S sequences:

1) The RDPclassifier provides the training data, where the taxonomy information is in the FASTA header: https://sourceforge.net/projects/rdp-classifier/files/RDP_Classifier_TrainingData/. The main RDPclassifier .jar file also has rm-dupseq and rm-partialseq functions to filter for unique sequences.

2) NCBI provides some 16S sequences in a BLAST database. It takes a little extra work to extract the FASTA sequence from the database files (using blastdbcmd -entry all -db 16SMicrobial > NCBI_16S.fa) and then download the taxonomy information, but BLCA provides some scripts for this pre-processing step: https://github.com/qunfengdong/BLCA

Last time I checked, the SILVA database had a different data format that was a little harder to parse, but taxonomy information is available in a format that can be used by mothur here: https://www.mothur.org/wiki/Silva_reference_files

ADD COMMENTlink written 2.5 years ago by Charles Warden7.5k
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