4-1 Sequence Alignment and Comparison

The comparison of one nucleotide or amino-acid sequence with another to find the degree of similarity between them is a key technique in present-day biology. A marked similarity between two gene or protein sequences may reflect the fact that they are derived by evolution from the same ancestral sequence. Sequences related in this way are called homologous and the evolutionary similarity between them is known as homology. Unknown genes from newly sequenced genomes can often be identified by searching for similar sequences in databases of known gene and protein sequences using computer programs such as BLAST and FASTA. Sequences of the same protein from different species can also be compared in order to deduce evolutionary relationships. Two genes that have evolved fairly recently from a common ancestral gene will still be relatively similar in sequence to each other; those that have a more distant common ancestor will have accumulated many more mutations, and their evolutionary relationship will be less immediately obvious, or even impossible to deduce from sequence alone.