This second edition provides new and updated chapters covering computational and mathematical techniques and concepts related to the field of comparative genomics. The topics covered in the chapters range from those that address general techniques and concepts that apply to all organisms to others that are specialized and apply to specific biological systems such as viruses, bacteria, nematodes, and insects. Well-known comparative genomics web-based platforms are also covered in specific chapters. Written in the highly successful Methods in Molecular Biology series format, many chapters include introductions to their respective topics and step-by-step comparison procedures, demonstrated on actual sets of genome sequences.
Authoritative and cutting-edge, Comparative Genomics: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.
The theory of gene family histories.- Protein-coding gene families in
prokaryote genome comparisons.- Family-free genome comparison.- Methods for
pangenomic core detection.- Step-by-step bacterial genome comparison.- How to
obtain and compare Metagenome-Assembled Genomes.- Comparative genome
annotation.- Annotation and comparative genomics of Prokaryotic Transposable
Elements.- Genome Rearrangement Analysis: Cut and Join Genome Rearrangements
and Gene Cluster Preserving Approaches.- AGO, a framework for the
reconstruction of ancestral syntenies and gene orders.- A guide to
phylogenomic inference.- Comparative RNA Genomics.- Bioinformatic approaches
for comparative analysis of viruses.- Comparative Analyses of Bacteriophage
Genomes.- Comparative genomics of sex, chromosomes, and sex chromosomes in
Caenorhabditis elegans and other nematodes.- Comparative evolutionary
genomics in insects.- Comparative Methods for Demystifying Spatial
Transcriptomics.- Comparative genomic analysis of bacterial data in BV-BRC:
an example exploring antimicrobial resistance.- VEuPathDB resources: a
platform for free online data exploration, integration, and analysis.- A
practical approach to using the Genomic Standards Consortium MIxS reporting
standard for comparative genomics and metagenomics.
