Running BLAST sequence similarity

BLAST is a program that compares a DNA/RNA or protein sequence, which are strings of letters against other reference sequences (i.e., whole non-redundant nucleic acid database, also known as NT).

Pre-requisites

• Installed conda3 or miniconda3 ( https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html ) → Recommend installing miniconda3 in your HPC’s /home directory.

• (optional) Basic unix command line knowledge (example: https://researchcomputing.princeton.edu/education/external-online-resources/linux ; https://swcarpentry.github.io/shell-novice/ )

• (optional) Familiarity with one unix text editors (example Vi/Vim or Nano):

  • VIM ( https://bioinformatics.uconn.edu/vim-guide/ ; https://missing.csail.mit.edu/2020/editors/)

  • Nano (https://engineering.purdue.edu/ECN/Support/KB/Docs/BasictutorialforNanou ; https://www.howtogeek.com/howto/42980/the-beginners-guide-to-nano-the-linux-command-line-text-editor/ )

• Have an HPC account on QUT’s lyra. Apply for a new HPC account here.

Install BLAST

Once miniconda3 has been installed. The first time you may need to reinitiate your terminal session to make the ‘conda’ command available.

To install BLAST or other bioinformatics tools go to https://anaconda.org and search for the tool of interest. If the tool is available click on the tool link, which will open a new window showing the command line needed to install the tool. For example for BLAST the suggested command is:

conda install -c bioconda blast

run the above command to install blast. Conda will evaluate if the tool or necessary dependencies are available and will automatically install all necessary items to run in this case blast.

Note: Follow a similar process as above to install other tools.