What is the purpose of a BLAST search and what outputs would you evaluate?

• A. To align protein structures; outputs include 3D coordinates.
• B. To find regions of similarity between sequences; outputs include alignments, E-values, percent identity, and query coverage.
• C. To synthesize DNA fragments in vitro.
• D. To measure gene expression levels.

Answer: (B)

BLAST searches are used to identify regions of similarity between biological sequences, which helps you spot potential homologs, infer function, and explore evolutionary relationships by comparing a query sequence against a database. When you run BLAST, you look at outputs that tell you how good the match is and how much of the query is involved. The alignment shows how the query and subject sequences line up, giving you a sense of conserved regions. The E-value indicates the probability that the observed similarity happened by chance; a smaller E-value means a more statistically meaningful hit. The percent identity tells you how similar the aligned residues or bases are, giving a measure of exact matches within the aligned region. The query coverage shows how much of your query is included in the alignment, which matters for understanding whether the match covers the whole sequence or just a fragment. Together, these outputs let you assess whether a match is biologically relevant and how it might relate to function or evolution. Other options describe different goals or outputs (for example, structural alignment yields 3D coordinates, DNA synthesis is a lab fabrication process, and gene expression measurement comes from expression assays), which are not what BLAST provides.