BLAST tutorial
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Run BLAST

Create a BLAST database

To put these various tools and options to use, let’s consider using blastp to look for proteins that are similar in sequence to other proteins in the yeast exome. For this tutorial, we’ll use the FASTA file orf_trans.fasta:

head orf_trans.fasta

In order to find sequences that are similar to others, we’re going to want to blastp this file against itself. So, we’ll start by creating a database of these sequences:

makeblastdb \
   -in orf_trans.fasta \
   -out orf_trans \
   -dbtype prot \
   -title "Yeast Open Reading Frames" \
   -parse_seqids \
   -blastdb_version 4

This will take a few seconds to complete.

Note: The -parse_seqids flag indicates that the sequence IDs from the FASTA file should be included in the database so that they can be used in outputs as well as by other tools

Once you run the command above, notice the new database files that were created:

ls -l
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