Why comparing sequences?
During evolution, random mutagenesis events take place at the DNA level, which change the gene sequences that encode for proteins. Some of these changes will make a protein non-functional, such as mutations of acitve site residues, or mutations that prevent the protein from folding correctly. Consequently, residues that are essential for a protein to function, or that are needed for the protein to fold correctly, are conserved over time. These residues can be detected by comparing related sequences and looking for those positions that remain the same in all the members of a protein family.
In this chapter, we go over the different existing techniques for aligning sequences, focusing on the dynamic programing techniques. We also cover FASTA and BLAST, as weel as study the statistics of sequence alignment.
Sequence versus structure alignment
The sequence of the ribonuclease F1 from fusarium monoliforme (FUS) is similar to the sequence of the ribonuclease from molsin (RDS). The alignment between these two sequences shows one insertion of two residues that translates into a longer loop in the structure of FUS, as seen in the structural alignment