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How to use BLAST to identify a viral sequence

This recipe demonstrates the use of BLAST to identify a viral sequence.

1 result • updated 5.1 years ago by Istvan Albert

This recipe demonstrates the use of BLAST to identify a viral sequence.

Suppose that you have a mystery sequence accessible at:

http://data.biostarhandbook.com/data/mystery1.fa

What is this sequence? What species can it be matched to? How similar is to the matched species?

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

# If you set the BLASTDB variable blast will look in that directory to find databases.
# Setting the BLASTDB variable is handy as it makes for shorter commands.
# It also allows for taxonomy information to be loaded if you have the taxdb installed there.

# Set the directory for storing BLAST databases in.
# We may repeatedly use databases, hence we store them
# outside the current project directory.
export BLASTDB=~/blastdb

# Make the BLAST database directory if it does not exist..
mkdir -p $BLASTDB

# The update_blast.pl code is not following proper UNIX standards.
# It exits with a nonzero status code even when it completes correctly (Thanks NCBI!).
# Hence we have to turn off the error watch for this line of code.
set +e

# Temporarily switch to the BLASTDB directory and run the blast database updater
# to download a viral reference database.
# The command will only update the blast database if it is incomplete or has changed.
(cd $BLASTDB && update_blastdb.pl --quiet --decompress ref_viruses_rep_genomes)

# When one or more commands are enclosed with parenthesis as above then a new bash shell
# is opened for the commands inside the parenthesis. This is why we don't have to change
# the directory back once we are done with the commands. Only the newly opened "child" bash
# shell will see the change directory command. The "parent" bash stays where it started.
# The && symbol is treated as a logical AND. Use it to list multiple commands on a single line.

# Turn the error watch back on.
set -e

# Get the "mystery sequence" from the book site.
wget -q -nc http://data.biostarhandbook.com/fasta/mystery1.fa

# We can list the short database name because BLASTDB is set properly
blastn -db ref_viruses_rep_genomes -query mystery1.fa > blast.results.1.txt

# If you did not set the BLASTB the same command would be:
# blastn -db ~/blastdb/ref_viruses_rep_genomes -query mystery1.fa > blast.results.1.txt

# We can format the output differently.
# Look at the blast -help for information on what each field means.
blastn -db ref_viruses_rep_genomes -query mystery1.fa -outfmt 7 > blast.results.2.txt

# We can also selectively output only certain columns:
# subject accession, query accession and percent identity.
# Look at blast --help for information on how to encode the format string.
blastn -db ref_viruses_rep_genomes -query mystery1.fa -outfmt "7 sacc qacc pident nident mismatch btop" > blast.results.3.txt

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[settings]
id = 99
recipe_uid = "recipe-blast-viral"
uid = "recipe-blast-viral"
name = "How to use BLAST to identify a viral sequence"
template = "How_to_use_BLAST_to_identify_a_viral_sequence_bio-data-analysis_99.sh"
image = "How_to_use_BLAST_to_identify_a_viral_sequence_bio-data-analysis_99.png"
project_uid = "bio-data-analysis"
url = "http://localhost8000"
help = "This recipe demonstrates the use of BLAST to identify a viral sequence.\n\nSuppose that you have a mystery sequence accessible at:\n\n* <http://data.biostarhandbook.com/data/mystery1.fa>\n\nWhat is this sequence? What species can it be matched to? How similar is to the matched species?\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/"

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