Protein BLAST Search

Overview

Teaching: 20 min
Exercises: 60 min

Questions

• How can similar protein sequences be identified using BLAST?

Objectives

• Students will explain how the results from sequence alignment scoring algorithms are generated and how this is used to identify similar sequences.

• Students will identify the limitations of the results provided by BLAST.

• Students will determine if a protein falls in a known superfamily of proteins.

• Students will determine which amino acids are conserved among (super)family members.

• Students will use BLAST searches along with structures, to determine which amino acids are not only in the active site, but which are conserved in the active site, and thus may be involved in catalysis.

• Students will evaluate the effect of “word size” on search results.

Modern biochemistry includes a wide variety of computational tools to characterize protein structure and function, and these tools must be included in modern biochemistry education. In this lab activity, we introduce students to BLAST (Basic Local Alignment Search Tool), one of the most popular sequence alignment tools. The basic syntax of running a BLAST search is presented, followed by a discussion of the interpretation of BLAST results. The students are then assigned a particular protein to study, generating BLAST results to identify a good match. In doing so, they must think about the algorithm parameters of BLAST and what parameters will give them the most useful results. This module can be used in conjunction with other bioinformatics modules from the BASIL group to identify the function of proteins of unknown function.

Module Resources

Access student module here

Key Points

• Protein BLAST searches identify sequence similarity between a query protein and a database of other proteins.

• Sequence similarity does not guarantee similarity in function.