New Bioinformatics Algorithms Applied to Deep Sequencing Projects
from: Advanced Vaccine Research Methods for the Decade of Vaccines (Edited by: Fabio Bagnoli and Rino Rappuoli). Caister Academic Press, U.K. (2015) Pages: 33-64.
Advances in high throughput sequencing technology have made significant contributions to research in genomics, epigenomics, and metagenomics. With abundant sequencing data currently available, we can now better investigate the dynamics of pathogen and host genomes, as well as their interactions within populations, to provide solid foundations for vaccine development and therapeutic research. In this chapter is provided an overview of bioinformatics algorithms developed for deep sequencing projects, in particular those related to vaccine development. These essential bioinformatics algorithms provide unprecedented opportunities to better understand the pathogens and human genomes, and their variants at single-nucleotide resolution. Many bioinformatics algorithms are also available for de novo identification and assembly of novel pathogen genomes and protein-coding genes. In order to catalogue the diverse immune repertoire, efficient bioinformatics algorithms have also been developed to detect recombination and hypermutations in T-cell receptors and antibodies. Current challenges in combining computational approaches to vaccine development and therapeutic research are also discussed read more ...