Benchmarking of alignment-free sequence comparison methods.

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.

Concl

SUBMITTER: Zielezinski A 

PROVIDER: S-EPMC6659240 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature