Epilogue: Multiple Sequence Alignment

Amino acid sequences of proteins performing the same function are likely to be somewhat similar, but these similarities may be elusive in the case of distant species. You now possess an arsenal of algorithms for aligning pairs of sequences, but if sequence similarity is weak, pairwise alignment may not identify biologically related sequences. However, simultaneous comparison of many sequences often allows us to find similarities that pairwise sequence comparison fails to reveal. Bioinformaticians sometimes say that while pairwise alignment whispers, multiple alignment shouts.

Building a three-dimensional Manhattan

We’re now ready to use pairwise sequence analysis to build up our intuition for comparison of multiple sequences. In our three-way alignment of A-domains from the introduction, we found 19 conserved columns: