Presents practical approaches to the pervasive question of how to choose parameter settings for sequence alignment
Provides links to proven software implementations that work well on real data
Introduces a general framework for parameter advising of broad utility in bioinformatics and beyond
Dan DeBlasio
Bioinformatics Biological sequence analysis Multiple sequence alignment Protein sequence alignment Alignment accuracy Alignment scoring parameters Substitution matrices Gap penalties Refining alignments Machine learning Ensemble methods Computational complexity Approximation algorithms Linear programming Integer linear programming