More on BLAST

 

There are many search programs in the BLAST suite, depending on the  type of analysis to be done, including:

  • blastn - Search a nucleotide database using a nucleotide query
    Methods: blastn, megablast, discontiguous megablast
  • blastp - Search protein database using a protein query
    Methods: blastp, psi-blast, phi-blast, delta-blast
  • blastx - Search protein database using a translated nucleotide query
  • tblastn - Search translated nucleotide database using a protein query
  • tblastx - Search translated nucleotide database using a translated nucleotide query
  • psiblast - Position-Specific Initiated BLAST
  • rpsblast - Reverse Position Specific BLAST
  • rpstblast - Translated Reverse Position Specific BLAST
  • deltablast - Domain enhanced lookup time accelarated BLAST

 

General Usage

 

Get help: To find the general usage of an individual program in the BLAST suite, use the -help flag. For example:

blastn -help

 

Convert  your data to blast format:  To run blast using your own fasta formatted sequence collection as a database, make sure that the database is converted to blast format prior to running the blast command. The program that does blast database formating from a fasta sequence collection is called "makeblastdb". For example:

makeblastdb -in uniprot_sprot.fasta -dbtype prot

 

Run BLAST: After the database is formatted, run the desired blast program. For example:

blastp -query myquery.fasta -num_threads 16 -db uniprot_sprot.fasta -out blastp.out

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