Running Command-Line BLAST¶
BLAST is the Basic Local Alignment Search large sequence databases; It starts by finding small matches between the two sequences and extending those matches. For in-depth information on how BLAST works and the different BLAST functionality, check out the resources page.
BLAST can be helpful for identifying the source of a sequence or finding a similar sequence in another organism. In this lesson, we will use BLAST to find zebrafish proteins that are similar to a small set of mouse proteins.
Why use the command line? BLAST has a very nice graphical interface for searching sequences in NCBI's database. However, running BLAST through the commmand line has many benefits:
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It's much easier to run many BLAST queries using the command line than the GUI
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Running BLAST with the command line is reproducible and can be documented in a script
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The results can be saved in a machine-readable format that can be analyzed later
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You can create your own databases to search rather than using NCBI's pre-built databases
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It allows the queries to be automated
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It allows you to use a remote computer to run the BLAST queries
| Est. time | Lesson name | Description |
|---|---|---|
| 30 mins | Install BLAST | Set up local BLAST installation on your computer |
| 15 mins | How to Run BLAST+ | Run BLAST analysis with AWS |
Learning Objectives
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Gain hands-on exposure to the linux command line
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Understand how data is turned into results by programs run at the command line
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Some expertise in biology and genetics.
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This tutorial was written to be run from an AWS remote instance. You need an AWS account. Please see our tutorial on setting up an AWS instance for help.
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Basic shell scripting knowledge. Users must be comfortable with finding and opening a terminal window.
Vidlet: BLAST tutorial walk-through