From NCBI Taxonomy to 16s RNA (automated)
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?
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Can you post a few examples of the NCBI IDs that you have?
243164 194424 216389
https://www.ncbi.nlm.nih.gov/taxonomy/?term=216389
Are you able to use these IDs to locate the 16s RNA sequences of interest on NCBI website?
You could use NCBI eutils to get all rRNA sequences and then filter out 16S sequences based on the descriptions:
However, this query would fail if 16S is written as 16s in the description.
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.
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]