BLAST Basics

What is BLAST?

• BLAST is an acronym for Basic Local Alignment Search Tool
  • Pub: Altschul, S F et al.
    “Basic local alignment search tool.” Journal of molecular biology vol. 215,3 (1990): 403-10. PMID: 2231712
• A tool for searching databases of biological sequences, DNA or protein, using a sequence as a query
• Matches and aligns regions of biological sequences: DNA-DNA, Protein-Protein
• Programs:
  • protein query, protein database
    • blastp, psi-blast
  • nucleotide query, nucleotide database
    • megablast, blastn
  • translating searches (useful for unannotated sequences)
    • protein query, nucleotide database: tblastn
    • nucleotide query, protein database: blastx
    • nucleotide query, nucleotide database: tblastx
• BLAST is the most widely used sequence similarity search tool in the world
• Web interfaces to databases at NCBI and many sites around the world
• Standalone tool and BLAST-ready databases available for download from NCBI

What does BLAST do?

• Finds high scoring local alignments between two sequences (protein or DNA)
• Includes a model of score distributions for random local alignments
• Provides statistical significance for matches / alignments
• BLAST returns non-chance similarities between biological sequences.
  • If similarities are not due to chance, then they must be due to something else!
    • Evolutionary relatedness (homology)
    • Simple identification

How and why do people use BLAST?

1. 1. Database searches

      1. To find homologs in other species, model organisms
         • Homology is related to function
           • A human protein that is a significant match to a yeast protein may have similar functions in both
           • Homology is not a guarantee of the same function. Conversely proteins with similar functions may not be evolutionarily related.
             • wings of birds, forelimb of mammals (homologs with related but not (exactly) the same function)
             • wings of butterflies vs. wings of birds (not homologs but with similar function)
      2. To identify a sequence — is this sequence already in the database and what is it?
      3. To identify or classify an organism from a sequence
         • environmental samples, organism associated metagenomes
         • specialized queries and databases: Targeted loci, barcode sequence (rRNA genes, cytochrome oxidase)

   2. Alignment tool

      • To quickly align, match up positions in related sequences

   3. Alignment plus database searches

      • To annotate other sequences (find genes, identify exons)
        • Aligning mRNA to genomic DNA
        • Matching proteins to genomic translations