Alignment-free sequence comparison: benefits, applications, and tools

Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. The strength of these methods makes them particularly useful for next...

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Bibliographic Details
Published in:Genome Biology 2017-10, Vol.18 (1), p.186-186, Article 186
Main Authors: Zielezinski, Andrzej, Vinga, Susana, Almeida, Jonas, Karlowski, Wojciech M
Format: Article
Language:English
Subjects:
Algorithms
Bioinformatics
Data processing
Fourier transforms
Genomes
Genomics
High-Throughput Nucleotide Sequencing
HIV
Human immunodeficiency virus
Information Theory
Mutation
Next-generation sequencing
Nucleotide sequence
Phylogenetics
Phylogeny
Protein families
Proteins
Proteomics
Review
Sequence Alignment
Sequence Analysis - methods
Sequence Homology
Software
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Summary:Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. The strength of these methods makes them particularly useful for next-generation sequencing data processing and analysis. However, many researchers are unclear about how these methods work, how they compare to alignment-based methods, and what their potential is for use for their research. We address these questions and provide a guide to the currently available alignment-free sequence analysis tools.
ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-017-1319-7