NCBI Standalone BLAST

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Using the standalone NCBI BLAST

I am describing the use of a standalone BLAST () on a Ubuntu 22.04.4 LTS system. You can get a lot of details at the NCBI BLAST Manual site . I will stick to the components i require for my work.

Building a BLAST database from local sequences

  • The makeblastdb application produces BLAST databases from FASTA files. 
  • Use the –parse_seqids flag when invoking makeblastdb to enable retrieval of sequences based upon sequence identifiers. It is possible to fetch individual sequences using blastdbcmd or to limit the search with the –seqidlist option.  In this case, each sequence must have a unique identifier, and that identifier must have a specific format. The identifier should begin right after the “>” sign on the definition line, contain no spaces.
  • specify its type (-dbtype nucl/prot)
  • name the output database with the same base name (-out hs_chr) overwriting the existing one.
  • -title for name of the Database
makeblastdb -in <sequence> -parse_seqids -dbtype prot -out <name> -title "<name>"

We can check the “re-created” database to find out if the masking information was added properly, using blastdbcmd with the following command line:

$ blastdbcmd -db <name> -info

Doing BLAST

blastp -query <file> -db <blast database> -out <output file> -evalue <Real> -outfmt 7

Extract data from BLAST databases using blastdbcmd

The following examples show how to extract selected information from a BLAST database. Extract the accession, sequence length, and masked locations for GI 71022837: 
$ blastdbcmd -entry 71022837 -db Test/mask-data-db -outfmt "%a %l %m" XP_761648.1 1292 119-139;140-144;147-152;154-160;161-216;

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