Learn to run BLAST with custom organism databases: setting up your environment, preparing and formatting databases, running searches, and reviewing results effectively.
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Prepare Your Environment
Prepare the Custom Database
Format the Custom Database
makeblastdb
tool from the BLAST+ suite to convert your FASTA file into a BLAST database.
input.fasta
with your FASTA file, and db\_name
with your chosen database name:
makeblastdb -in input.fasta -dbtype nucl -out db\_name
-dbtype
option to specify whether your sequences are nucleotide (nucl
) or protein (prot
).
Prepare Your Query Sequence
Run BLAST Search
blastn
command for nucleotide queries or blastp
for protein queries.
query.fasta
with your query file, db\_name
with your database name, and output.txt
with your desired output file:
blastn -query query.fasta -db db\_name -out output.txt
-evalue
for setting an E-value threshold or -outfmt
for different output formats.
Review Results
output.txt
) to review your BLAST results.
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