Format

Send to

Choose Destination
Genome Biol. 2017 Oct 3;18(1):186. doi: 10.1186/s13059-017-1319-7.

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

Author information

1
Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland.
2
IDMEC, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001, Lisbon, Portugal.
3
Stony Brook University (SUNY), 101 Nicolls Road, Stony Brook, NY, 11794, USA.
4
Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland. wmk@amu.edu.pl.

Abstract

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.

PMID:
28974235
PMCID:
PMC5627421
DOI:
10.1186/s13059-017-1319-7
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center