Extending the Core Problems
In this chapter we look in detail at alignment problems in the more complex contexts typical of string problems that currently arise in computational molecular biology. These more complex problems require techniques that extend (rather than refine) the core alignment methods.
13.1. Parametric sequence alignment
When using sequence alignment methods to study DNA or amino acid sequences, there is often considerable disagreement about how to weight matches, mismatches, insertions and deletions (indels), and gaps. The most commonly used alignment software packages require the user to specify fixed ...