Blast practice

Blast with NCBI

  • Go to NCBI
  • Click Protein BLAST
  • upload sopD_proteinfasta file, choose the database swissprot, click Algorithm parameters at the bottom, check all the options. Click BLAST
  • The BLAST may run for a while. Check the results:
    • How many hits are there?
    • Check the Query cover, E value, Per. Idet. How many hits have a E-value lower than 10e-6? What does this mean?
    • Click the second alignment. How many Identities, Positives and Gaps?

Run a local Blast

  • Use Filezilla, upload sopD_gene.fasta, salmonella_typhimurium_lt2.fasta to server.

  • Run Blast from your conda virtual environment:

      conda activate bioinfo
  makeblastdb -in sopd_gene.fasta -dbtype nucl -out sopD
  blastn -query salmonella_typhimurium_lt2.fasta -db sopD -out sopD_lt2.txt -outfmt 1

    Read the help document of each program before you run it. Make sure you understand all the parameters you typed in.

    After the program completes, read the output file sopD_lt2.txt

    Try another output format:

      blastn -query salmonella_typhimurium_lt2.fasta -db sopD -out sopD_lt2_fmt6.tsv -outfmt 6

Visualise the blast results

  • Run act on your laptop
  • Click File -Open, open sopd_gene.fasta as sequence 1, sopD_lt2_fmt6.tsv as comparison file, salmonella_typhimurium_lt2.fasta as sequence 2.
  • When the act window open, use the scrollbar at top-right to zoom in. Double click the red bar in the middle, to put the match sequence in the center. What is the position of Salmonella Typhimurium genome that matches the sopD gene?