How a 1990 algorithm traces the evolutionary footprints of ancient humans
In short: When scientists discover a new gene, they face a massive puzzle: where does it fit in the tree of life? The answer lies in BLAST, a high-speed heuristic algorithm that scans vast genomic databases to find hidden similarities between proteins and DNA.
Developed in 1990 by a team at the NIH including Eugene Myers and Stephen Altschul, the Basic Local Alignment Search Tool (BLAST) revolutionized bioinformatics. While older methods like the Smith-Waterman algorithm guarantee the mathematically optimal alignment, they are too computationally expensive for modern genomic scales. BLAST uses a heuristic approach, prioritizing speed by searching for significant patterns. This efficiency allows researchers to compare a query sequence against massive databases, such as the ClusteredNR database, to identify functional and evolutionary relationships.
The power of BLAST is most evident when tracing human lineage. By comparing mitochondrial DNA—which is inherited maternally and has a low recombination rate—researchers can map the connections between modern humans (Homo sapiens) and extinct relatives. For instance, comparing the modern human mitochondrial genome (NC_012920.1) against Neanderthal (NC_011137.1) and Denisovan (NC_013993.1) sequences reveals striking similarities. Comparing sequences via BLAST reveals that Neanderthal DNA shares roughly 99% identity with modern humans, while Denisovan DNA shows 98% similarity.
These alignments do more than show similarity; they pinpoint the exact mutations that define a species. A single nucleotide substitution, such as thymine at position 3108 in humans replacing cytosine in Neanderthals, can change an amino acid from threonine to methionine. Such precise, base-by-base comparisons allow scientists to investigate whether mutations are conservative or non-conservative, ultimately helping us understand how subtle genetic shifts influence protein structure and the broader evolution of life.
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Sources
- Summary by Intellect · source: BLAST: Compare & identify sequences - NCBI Bioinformatics Resources: An Introduction - Library Guides at UC Berkeley
- Also: BLAST (biotechnology)
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