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.
journal_name
Brief Bioinformjournal_title
Briefings in bioinformaticsauthors
Song K,Ren J,Reinert G,Deng M,Waterman MS,Sun Fdoi
10.1093/bib/bbt067subject
Has Abstractpub_date
2014-05-01 00:00:00pages
343-53issue
3eissn
1467-5463issn
1477-4054pii
bbt067journal_volume
15pub_type
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pub_type: 杂志文章
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pub_type: 杂志文章,评审
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更新日期:2015-01-01 00:00:00
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pub_type: 杂志文章
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