New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing.
Brief Bioinform
; 15(3): 343-53, 2014 May.
Article
em En
| MEDLINE
| ID: mdl-24064230
ABSTRACT
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.
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Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Análise de Sequência
/
Biologia Computacional
Tipo de estudo:
Health_economic_evaluation
/
Risk_factors_studies
Idioma:
En
Revista:
Brief Bioinform
Assunto da revista:
BIOLOGIA
/
INFORMATICA MEDICA
Ano de publicação:
2014
Tipo de documento:
Article