4.5.6. Search database using query sequence#

With the query sequence downloaded and the database downloaded and formatted, you can start performing a BLAST search.

First, change into the directory containing the query sequence:

cd ~/projects/sars-cov-2

Now run the blastp command using the query sequence and the complete path to the database:

blastp -query P0DTC2.fasta \
-db /home/user/databases/swissprot \
-out blastp-results.txt \
-outfmt "7 sacc stitle qlen slen pident"

What the options mean:

-query

Path to the query sequence.

-db

Complete path of the sequence database.

-out

File to save results to.

-outfmt

Format of the output file. This will use format option 7 (tab-delimited text) and include the following information:

  • accession number and description of matching sequences (sacc and stitle),

  • query and subject sequence lengths (qlen and slen)

  • percentage identity of the match (pident).

When the database search is complete, you can open blastp-results.txt to view the results:

less -S blastp-results.txt

The -S option of the less command disables word-wrap.

Output:

# BLASTP 2.9.0+
# Query: sp|P0DTC2|SPIKE_SARS2 Spike glycoprotein OS=Severe acute respiratory syndrome coronavirus 2 OX=2697049 GN=S PE=1 SV=1
# Database: /home/user/databases/swissprot
# Fields: subject acc., subject title, query length, subject length, % identity
# 88 hits found
P0DTC2      Spike glycoprotein OS=Severe acute respiratory syndrome coronavirus 2 OX=2697049 GN=S PE=1 SV=1 1273    1273    100.000
P59594      Spike glycoprotein OS=Severe acute respiratory syndrome coronavirus OX=694009 GN=S PE=1 SV=1    1273    1255    76.038
Q3LZX1      Spike glycoprotein OS=Bat coronavirus HKU3 OX=442736 GN=S PE=3 SV=1     1273    1242    76.041
Q3I5J5      Spike glycoprotein OS=Bat coronavirus Rp3/2004 OX=349344 GN=S PE=1 SV=1 1273    1241    75.334
Q0Q475      Spike glycoprotein OS=Bat coronavirus 279/2005 OX=389167 GN=S PE=3 SV=1 1273    1241    74.745
...