Evolutionary Genomics pp 237-257

Part of the Methods in Molecular Biology book series (MIMB, volume 855) | Cite as

Whole-Genome Alignment

Protocol

Abstract

Whole-genome alignment (WGA) is the prediction of evolutionary relationships at the nucleotide level between two or more genomes. It combines aspects of both colinear sequence alignment and gene orthology prediction, and is typically more challenging to address than either of these tasks due to the size and complexity of whole genomes. Despite the difficulty of this problem, numerous methods have been developed for its solution because WGAs are valuable for genome-wide analyses, such as phylogenetic inference, genome annotation, and function prediction. In this chapter, we discuss the meaning and significance of WGA and present an overview of the methods that address it. We also examine the problem of evaluating whole-genome aligners and offer a set of methodological challenges that need to be tackled in order to make the most effective use of our rapidly growing databases of whole genomes.

Key words

Sequence alignment Whole-genome alignment Orthology map Toporthology Genome evolution Comparative genomics 

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Biostatistics and Medical Informatics and Computer Sciences, Genome Center of WisconsinUniversity of Wisconsin-MadisonMadisonUSA

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