Sequence Alignment and BLAST

One-Sentence Definition

Sequence alignment finds homologous positions between DNA/protein strings; BLAST is a fast heuristic search that ranks similar sequences in large databases.

Simple Explanation

Alignment = line up letters to see matches. BLAST = Google search for similar genes/proteins.

Detailed Scientific Explanation

• Pairwise vs multiple sequence alignment (MSA)
• Local (Smith–Waterman / BLAST) vs global (Needleman–Wunsch)
• BLAST flavors: blastn, blastp, blastx…
• In micro: species ID (16S), AMR gene detection, annotation transfer
• Modern alternatives/complements: HMMER (profiles), DIAMOND (fast protein), mash (whole-genome sketches), MMSeqs2

Mechanism

Seed hits → extension → scoring matrix + gap penalties → E-value ranks chance expectation.

Clinical Importance

• Interpreting “99% identity to blaKPC-2” style reports
• Bad E-value thresholds → false AMR calls

Research Importance

• Phylogenetic character matrices; ortholog detection

Diagnostic Relevance

• Underpins many AMR Gene Databases search engines and 16S ID

AMR Relevance

• Hit identity/coverage thresholds define gene presence calls

Related Methods

• PCR primer design · Whole-Genome Sequencing annotation

Related MOCs

• MOC - Bioinformatics in Microbiology · MOC - Antimicrobial Resistance (AMR)

Active Recall Questions

1. What does an E-value mean intuitively?
2. blastn vs blastp?
3. Why isn’t raw %identity enough without coverage?

Connections

• Genome Assembly · AMR Gene Databases · Carl Woese