Question: From NCBI Taxonomy to 16s RNA (automated)
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gravatar for Benni
12 months ago by
Benni30
Benni30 wrote:

I have a list of NCBI Taxonomy IDs and I want to retrieve the corresponding 16S RNA sequence. I can do this for every single element using SILVA https://www.arb-silva.de/. But I need an automated way. As far as I know, SILVA does not have an REST API, but maybe other databases are accessible in a programmatic way?

16s rna taxonomy • 513 views
ADD COMMENTlink written 12 months ago by Benni30

Can you post a few examples of the NCBI IDs that you have?

ADD REPLYlink written 12 months ago by Sej Modha4.2k

243164 194424 216389

https://www.ncbi.nlm.nih.gov/taxonomy/?term=216389

ADD REPLYlink modified 12 months ago • written 12 months ago by Benni30

Are you able to use these IDs to locate the 16s RNA sequences of interest on NCBI website?

ADD REPLYlink modified 12 months ago • written 12 months ago by Sej Modha4.2k

You could use NCBI eutils to get all rRNA sequences and then filter out 16S sequences based on the descriptions:

esearch -db nuccore -query "txid243164[Organism:noexp] AND biomol_rrna[PROP] AND 16S"|efetch -format fasta

However, this query would fail if 16S is written as 16s in the description.

ADD REPLYlink written 12 months ago by Sej Modha4.2k

I downloaded the 16S RefSeq Nucleotide sequence records. https://www.ncbi.nlm.nih.gov/nuccore?term=33175%5BBioProject%5D+OR+33317%5BBioProject%5D They contain the information I need.

ADD REPLYlink written 12 months ago by Benni30
1

They also contain a bunch of DNA sequences, more precise link would be: https://www.ncbi.nlm.nih.gov/nuccore?term=33175[BioProject]%20OR%2033317[BioProject]%20AND%20biomol_rrna[PROP]

ADD REPLYlink written 12 months ago by Sej Modha4.2k
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