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How to build and use BLAST databases

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

1 result • updated 13 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.

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# Stop script on any error.
set -ux

# 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 16SMicrobial -info > database.info.txt

# Get all the sequences out of the database
blastdbcmd -db 16SMicrobial -entry all > database.all.fa

# Get just one sequence ouf the the database.
blastdbcmd -db 16SMicrobial -entry NR_026093 > database.sequence.NR_026093.fa

# Get just the first 20 bases of all sequences ouf the the database.
blastdbcmd -db 16SMicrobial -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 16SMicrobial -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 16SMicrobial -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 16SMicrobial -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

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[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"

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                        [size]
                        label = "Window size"
                        display = "INTEGER"
                        value = 100
                        range = [1, 100]
                        help = "Selects the smoothing window."

Float values

                        [cutoff]
                        label = "P_Value Cutoff"
                        display = "FLOAT"
                        value = 0.05
                        range = [0, 1]
                        help = "Selects the cutoff."

Text box

                    [sra]
                    label = "Run Number"
                    display = "TEXTBOX"
                    value = "SRR519926"
                    regex = 'SRR\d+'
                    help = "Please provide SRR Run number"

Dropdown menu

                    [color]
                    label = "Select color"
                    display = "DROPDOWN"
                    choices = [ ["R","Red"], ["B","Blue"] ]
                    value = "R"
                    help = "Select a color of your choice"

Check box

                    [validate]
                    label = "Cross Validate"
                    display = "CHECKBOX"
                    value = true
                    help = "Apply cross validation on the results."

Upload Field

                    [file]
                    label = "Upload a file "
                    display = "UPLOAD"
                    help = "Upload a file to analyze"

Pick Data

                    [data]
                    label = "Pick data"
                    source = "PROJECT"
                    help = "Pick data from this project."

Radio Buttons

                    [species]
                    label = "Select species"
                    display = "RADIO"
                    choices = [ ["c","Cat"], ["d","Dog"] ]
                    value = "c"
                    help = "Select the species."

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