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How to inspect the contents of a BLAST databases

This recipe demonstrates the utility of blast databases for manipulating sequences.

1 result • updated 2.4 years ago by Istvan Albert

This recipe demonstrates the utility of blast databases for manipulating sequences.

BLAST databases can be useful in many other contexts.

For more information see the

Bioinformatics Data Analysis oline course
Biostar Handbook for system setup and other information.

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# Stop script on any error.
set -uex

# The name of the BLAST database
DBNAME=16S_ribosomal_RNA

# This will be the directory we store BLAST databases in.
export BLASTDB=~/blastdb

# Make the BLAST database directory.
mkdir -p $BLASTDB

# The update_blastdb.pl script is behaving oddly. 
# Will raise error exit code even when the process completes with no error.
# Need to turn off automatic exit on error.
set +e

# Temporarily switch to the BLASTDB directory and run the blast database updater.
# It will only update the data if it is incomplete or has changed.
(cd $BLASTDB && update_blastdb.pl --quiet --decompress $DBNAME)

# Turn strict error checking back on.
set -e

# What is inside of this database?
blastdbcmd -db $DBNAME -info 

# Get just one sequence ouf the the database.
blastdbcmd -db $DBNAME -entry NR_026093 > data-single.fa

# Get just the first 20 bases of all sequences ouf the the database.
blastdbcmd -db $DBNAME -entry all -range 1-20 > data-ranges.fa
echo " "

# Get just the first 20 bases of a given sequence ouf the the database.
blastdbcmd -db $DBNAME -entry NR_026093 -range 1-20 > data-subset.fa
echo " "

# Get all the sequences out of the database.
blastdbcmd -db $DBNAME -entry all > data-all.fa

# We can also format the output using a format string.
#
# See blastdbcmd -help for the -outfmt parameter
#
# List the lenght of each sequence in the database
blastdbcmd -db $DBNAME -entry all -outfmt "%a %l" > data-table.txt

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