Bioinformatics Recipe Cookbook

Recipe Description

The recipe demonstrates the utility of blast databases for manipulating sequences. Blast databases are typically used only to run BLAST searches.

As it turns out they are quite useful in many other contexts.

Recipe Code | Recipe Description

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#!/usr/bin/env bash

# Stop script on any error.
set -ue

# If you set the so called BLASTDB variable
# blast will find the files there automatically.
# This is handy as it makes for shorter commands.

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

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

# 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 --decompress 16SMicrobial)

#
# By default the blastdbcmd produces FASTA output
#

# When we know the accession number we can query for one specific entry.
echo ""
echo "*** The first ten lines of accession number NR_026093"
blastdbcmd -db 16SMicrobial -entry NR_026093 | head

# We can limit the sequence length.
echo ""
echo "*** Limit to the first 20 bases:"
blastdbcmd -db 16SMicrobial -entry NR_026093 -range 1-20

# We can also extract all entries from the database.
echo ""
echo "*** Dump all sequences of the database into file all.fa"
blastdbcmd -db 16SMicrobial -entry all > all.fa

# We can also format the output using a format string.
#
# See blastdbcmd -help for the -outfmt parameter
#
echo ""
echo "*** Format the output using a format string: accession number and sequence length"
blastdbcmd -db 16SMicrobial -entry all -range 1-20 -outfmt "%a %l" > acc.txt

# Show the first ten lines.
cat acc.txt | head

# How many genes are there
echo ""
echo "*** How many database sequences in the database"
blastdbcmd -db 16SMicrobial -entry all -range 1-20 -outfmt "%a" | wc -l

# Since these are 16SMicrobial genes that are highly conserved
# let's find out the variety we can see within 20 bases.
# What are the top ten most common gene starts and how many of each?
echo ""
echo "*** Top 10 common gene sequence starts:"
blastdbcmd -db 16SMicrobial -entry all -range 1-20 -outfmt "%s" | sort | uniq -c | sort -rn > common.txt

# Show the first ten common starts.
cat common.txt | head

#
# How to we build a new blast database from sequences.
#
# Use the all.fa file to create a new blast database.
#

# Create a directory that will store the blast database.
mkdir -p xdb

# Generate the new blast database
echo ""
echo "*** Building the blast database"
makeblastdb -dbtype nucl -in all.fa -parse_seqids -out xdb/my16S

# Demonstrates how the new database has the same content"
echo ""
echo "*** Top 10 common gene sequence starts using the newly created database:"
blastdbcmd -db xdb/my16S -entry all -range 1-20 -outfmt "%s" | sort | uniq -c | sort -rn | head

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