A Query for ATCC Genomic Sequences

Question

[Steven Lakin]

Hello,

Is there a resource or standard way to subset any of the nucleotide databases specifically to the reference/standard ATCC organisms? For my particular application, I'm interested in antimicrobial resistant strains, but any way to subset on the larger group of genomic sequences that are also available as ATCC samples would be appreciated.

Thanks

[GenoMax]

Depending on how many you need that are in NCBI genome database it may be better to construct a database by grabbing the data you need from NCBI (warning: this is a large directory) rather than trying to make a subset from a pre-formatted NCBI database.

Answer 1

[piet]

Strain collections like ATCC do not sequence their isolates (yet). All full genome sequences of ATCC organismens have been submitted by third parties and the metadata of such sequences in Genbank is very inconsistent.

You may query either the nucleotide or the biosample database with a search term such as 'ATCC[All Fields] AND "Streptococcus pneumoniae"[Organism]'. The number of hits is reduced by restricting the search to a single species. But this is a heuristic approach and there is no warranty to find all sequences available.

These links show the results of such a search:

• https://www.ncbi.nlm.nih.gov/biosample/?term=(ATCC)+AND+%22Streptococcus+pneumoniae%22%5BOrganism%5D
• https://www.ncbi.nlm.nih.gov/nucleotide/?term=(ATCC)+AND+%22Streptococcus+pneumoniae%22%5BOrganism%5D