Recipe View

How to build and use BLAST databases

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

1 result • updated 15 months 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.

Copy recipe

You need write access to the project to edit.

# Stop script on any error.
set -ux

# 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

# 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 16SMicrobial)

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

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

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

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

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

#
# Since these are 16SMicrobial genes that are highly conserved sequence starts?
#

# What are the top ten most common gene starts and how many of each?
blastdbcmd -db $DBNAME -entry all -range 1-20 -outfmt "%s" | sort | uniq -c | sort -rn > database.starts.txt

# Count how many times does each 16S gene starts with a sequence.
cat database.starts.txt | sort | uniq -c | sort -rn > database.sequence.starts.common.txt


#
# 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 newdb

# Create a  new blast database.
makeblastdb -dbtype nucl -in  database.all.fa -parse_seqids -out newdb/my16S

# How many sequences in the new database?
blastdbcmd -db newdb/my16S -info > newdb.info.txt

You need write access to the original recipe to edit.

Click the buttons on the right to create new fields.

Add text field Add float field Add data field Add checkbox Add dropdown Add upload field Add integer field Add radio button

Edit the content of each interface element.

[settings]
name = "How to build and use BLAST databases"
help = "This recipe demonstrates the utility of blast databases for manipulating sequences.\n\nBLAST databases can be useful in many other contexts.\n\nFor more information see the \n\n* [Bioinformatics Data Analysis][link] oline course\n* [Biostar Handbook][book] for system setup and other information.\n\n[link]: https://www.biostarhandbook.com/edu/course/4/\n[book]: https://www.biostarhandbook.com/"
template = "How_to_build_and_use_BLAST_databases_bio-data-analysis_90.sh"
image = "How_to_build_and_use_BLAST_databases_bio-data-analysis_90.png"
id = 90
recipe_uid = "recipe-blast-db"
uid = "recipe-blast-db"
url = "http://localhost8000"

You need write access to the original recipe to edit.

Name

Recipe display name

Identifier

Unique identifier for the recipe.

Image :

Optional image for the recipe ( 500px Maximum ).

Rank:

Used to order recipes (optional).

Insert Image

From the web

From your computer

Cancel

Back