NCBI: Retrieve Sequences for an Organism
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NCBI: Retrieve Sequences for an Organism


This tutorial follows closely to How To called “Retrieve all sequences for an organism or taxon.” It might also be called, How To find the sequence record types available for a given organism or taxon. Let’s see what record types are available for mouse. I’ll search the Taxonomy database directly by first selecting Taxonomy in the pull-down menu, then typing mouse and clicking Search. You can also search by scientific name. Clicking on Mus musculus takes us to a Taxonomy Browser page
showing all the subspecies. I’ll click on Mus musculus, but clicking on any of the subspecies names
would also get you to a summary table of sequence records. Here’s the summary table where the Subtree links column includes numbers for all of the subspecies. So if I wanted the set of solved structure records, for example, I’d click on one of the numbers in the Structure
row, which takes me to the Entrez Structure database
records. Now I’ll go back. If I want the set of Reference Sequence chromosome
records, I click on the links in the Genome Sequences
row. Ror large numbers of records, you probably cannot download the complete
set in your browser. See the Entrez Programming Utilities, or E-Utilities, in the How To called, “Download a large custom set of records from NCBI.”

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