Sequence alignment and comparison
Comparing sequences is the core tool of bioinformatics. Similar sequences often mean similar functions and shared ancestry.
Why compare sequences
Genes that share ancestry tend to keep similar sequences because important functions are preserved. If a newly found human gene closely matches a well-studied mouse gene, it probably does a similar job. Comparing sequences also reveals mutations linked to disease.
Homology
Sequences sharing a common ancestor are homologous. Orthologs are homologous genes in different species that separated when the species split, like human and mouse haemoglobin. Paralogs arose by duplication within one genome, like the different haemoglobin genes that work at different life stages.
Pairwise alignment
Alignment lines sequences up to show matching positions, inserting gaps where one sequence has extra bases. Scoring systems reward matches and penalise mismatches and gaps. Global alignment matches whole sequences end to end; local alignment finds the best-matching segments, useful when only part of a gene is shared.
BLAST
BLAST (Basic Local Alignment Search Tool) rapidly searches a database for sequences similar to a query. It reports matches ranked by score and an E-value, the number of matches that well expected by chance. A very small E-value, like 1e-50, means the match is almost certainly meaningful.
Multiple sequence alignment
Aligning many related sequences at once shows which positions are conserved, unchanged across species, often because they are critical for function. Positions that vary freely are less important. Conserved regions guide drug design and help predict which mutations will be harmful.
Building phylogenetic trees
Bioinformatics builds evolutionary trees from aligned sequences, grouping species whose sequences differ least. Methods include distance-based approaches and statistical methods like maximum likelihood. Molecular trees revealed, for example, that whales are closely related to hippos.
Tracking pathogens
Sequencing viruses and bacteria from patients lets scientists track outbreaks in real time. During the COVID-19 pandemic, millions of SARS-CoV-2 genomes were sequenced and shared, letting researchers spot new variants within weeks and trace how they spread.
Worked example
Compare two short sequences: ACGTTA and ACCTTA. Position by position: A=A, C=C, G vs C mismatch, T=T, T=T, A=A. That is 5 matches out of 6, or about 83% identity. In real comparisons, statistics like the E-value are needed to judge whether similarity is meaningful or chance.
Key takeaways
Similar sequences suggest shared ancestry and function. Orthologs split at speciation; paralogs by duplication. Alignment lines up sequences with gaps, scored by matches and penalties. BLAST searches databases and reports E-values. Multiple alignments reveal conserved regions. Sequence comparisons build phylogenies and track pathogens.
Flashcard
Share a common ancestor
Check your understanding
A BLAST search returns two hits with E-values of 1e-80 and 0.5. Which is more likely a true homolog?