Chapter

Constructing Alignment Benchmarks

Julie D. Thompson

in Sequence Alignment

Published by University of California Press

Published in print November 2009 | ISBN: 9780520256972
Published online March 2012 | e-ISBN: 9780520943742 | DOI: http://dx.doi.org/10.1525/california/9780520256972.003.0008
Constructing Alignment Benchmarks

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This chapter examines the increasing role of computer simulation in alignment evaluation, not just for the benchmarking of alignment algorithms but also for exploring the consequences of alignment errors (or use of alternate alignments) in bioinformatic analysis. The quality of an algorithm is often estimated by comparing the results obtained with a predefined benchmark, which provides a set of standard tests used to determine the relative performance of different programs. The chapter discusses multiple alignment benchmarks in detail, first discussing the criteria for benchmark development and issues involved in the definition of a multiple alignment benchmark. It concludes with a discussion on the evolution of multiple sequence alignments since the introduction of benchmarking, and the improvements achieved by the most recent methods.

Keywords: computer simulation; alignment evaluation; benchmarking; alignment algorithms; benchmarks; multiple alignment benchmarks

Chapter.  8353 words.  Illustrated.

Subjects: Evolutionary Biology

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