NCBI offers a a variety of resources that allow developers and other power users to access and manipulate information available in the NCBI databases. Visit the NCBI Develop page where you can access the listing of programming interfaces (APIs), Code Libraries, Data Formats and more. 

Consider using Entrez Programming Utilities (E-utilities) for searching, batch record retrieval, and linking between the records in the NCBI Entrez databases such as PubMed, Nucleotide, and Protein.  The E-utilities are nine server-side programs that function as the API for the Entrez system, and they work similarly to searches, linking and retrievals that you would perform on the web. As an alternative to the E-utilities URL interface, you may want to use Entrez Direct (EDirect), which provides the same set of services on the UNIX command line.

In addition to our E-utilities, which are available universally for the Entrez databases, you may find NCBI's specialized APIs useful. These include the PubChem Power User Gateway (PUG) or any of the PubMed Central (PMC) APIs.

For high-throughput sequence similarity searches (BLAST®) you can choose between the BLAST® URL API, Cloud BLAST, or the stand-alone BLAST applications (BLAST+).