Benchmarking of alignment-free sequence comparison methods
Zielezinski, Andrzej ; Girgis, Hani Z ; Bernard, Guillaume ; Leimeister, Chris-Andre ; Tang, Kujin ; Dencker, Thomas ; Lau, Anna K ; Röhling, Sophie et al.
Citable Link (URL):http://resolver.sub.uni-goettingen.de/purl?gs-1/16308
Abstract Background Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment. Results Here, we present a community resource (http://afproject.org) to establish standards for comparing alignment-free approaches across different areas of sequence-based research. We characterize 74 AF methods available in 24 software tools for five research applications, namely, protein sequence classification, gene tree inference, regulatory element detection, genome-based phylogenetic inference, and reconstruction of species trees under horizontal gene transfer and recombination events. Conclusion The interactive web service allows researchers to explore the performance of alignment-free tools relevant to their data types and analytical goals. It also allows method developers to assess their own algorithms and compare them with current state-of-the-art tools, accelerating the development of new, more accurate AF solutions.