New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing.
With the development of next-generation sequencing (NGS) technologies, a large amount of short read data has been generated. Assembly of these short reads can be challenging for genomes and metagenomes without template sequences, making alignment-based genome sequence comparison difficult. In addition, sequence reads from NGS can come from different regions of various genomes and they may not be alignable. Sequence signature-based methods for genome comparison based on the frequencies of word patterns in genomes and metagenomes can potentially be useful for the analysis of short reads data from NGS. Here we review the recent development of alignment-free genome and metagenome comparison based on the frequencies of word patterns with emphasis on the dissimilarity measures between sequences, the statistical power of these measures when two sequences are related and the applications of these measures to NGS data.
Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, USA. fsun@usc.edu or msw@usc.edu.
Kai
K
Song
Jie
J
Ren
Gesine
G
Reinert
Minghua
M
Deng
Michael S
MS
Waterman
Fengzhu
F
Sun
D000465:Algorithms; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D023281:Genomics / Q000379:methods / Q000706:statistics & numerical data; D059014:High-Throughput Nucleotide Sequencing; D008390:Markov Chains; D015233:Models, Statistical; D016415:Sequence Alignment; D017421:Sequence Analysis / Q000379:methods* / Q000706:statistics & numerical data
Markov model; NGS data; alignment-free; genome comparison; statistical power; word patterns