Multiple sequence analysis in the presence of alignment uncertainty

Thesis

Sequence alignment is one of the most intensely studied problems in bioinformatics, and is an important step in a wide range of analyses. An issue that has gained much attention in recent years is the fact that downstream analyses are often highly sensitive to the specific choice of alignment.

One way to address this is to jointly sample alignments along with other parameters of interest. In order to extend the range of applicability of this approach, the first chapter of this thesi...

Expand abstract

Authors: Herman, J; Joseph Herman

• Publication date: 2014
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: Oxford University, UK
• Language: English
• Keywords: Markov chain Monte Carlo; structural alignment; stochastic context-free grammars; graphical models; globin evolution; multiple sequence alignment; statistical alignment; sequence annotation; Bayesian phylogenetics; alignment uncertainty; directed acyclic graphs; hidden Markov models; RNA secondary structure
• Subjects: Probability; Bioinformatics (life sciences); Stochastic processes; Structural genomics; Mathematical genetics and bioinformatics (statistics)