Genomic Data Access Through BLAST

The BLAST programs from NCBI are popular tools for sequence analysis. The BLAST web service from NCBI combines these tools with a large collection of publicly available sequences as BLAST databases to meet different research goals. NCBI also provides standalone BLAST binaries that can search custom local databases or work as clients to search databases at the NCBI. In this talk, I will summarize the types of nucleotide databases available, their organization at NCBI, and how you can select the appropriate ones for your research using the BLAST web interface (http://blast.ncbi.nlm.nih.gov). For users with high throughput needs, I will present alternatives to the BLAST web interface for searching genomic data, including using the standalone BLAST+ package, its client function, and the vdb_blastn/vdb_tblastn from NCBI’s sratoolkit for next-gen reads. I will also demonstrate how to search and retrieve BLAST database information using the Entrez Utilities framework to choose the appropriate databases for these alternative BLAST avenues.