How to use BLAST+
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BLAST+ is a very widely used sequence alignment software, provided by NCBI.
BLAST+ is a very widely used sequence alignment software, available from NCBI and available for download at:
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
The method of use is as follows:
formatted database
makeblastdb -in db.fasta -dbtype prot -parse_seqids -out dbname
Parameter description:
-in: sequence file to be formatted
-dbtype: database type, prot or nucl
-out: database name
Protein sequence alignment protein database (blastp)
blastp -query seq.fasta -out seq.blast -db dbname -outfmt 6 -evalue 1e-5 -num_descriptions 10 -num_threads 8
Parameter description:
-query: Enter file path and file name
-out: Output file path and file name
-db: formatted database path and database name
-outfmt: output file format, there are 12 formats in total, 6 is tabular format corresponding to BLAST m8 format
-evalue: Set the e-value of the output result
-num_descriptions: the number of tabular output results
-num_threads: Number of threads
Nucleic acid sequence alignment nucleic acid database (blastn) and nucleic acid sequence alignment protein database (blastx)
Similar to blastp above:
blastn -query seq.fasta -out seq.blast -db dbname -outfmt 6 -evalue 1e-5 -num_descriptions 10 -num_threads 8
blastx -query seq.fasta -out seq.blast -db dbname -outfmt 6 -evalue 1e-5 -num_descriptions 10 -num_threads 8
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