Title |
Comparison of metagenomic samples using sequence signatures
|
---|---|
Published in |
BMC Genomics, December 2012
|
DOI | 10.1186/1471-2164-13-730 |
Pubmed ID | |
Authors |
Bai Jiang, Kai Song, Jie Ren, Minghua Deng, Fengzhu Sun, Xuegong Zhang |
Abstract |
Sequence signatures, as defined by the frequencies of k-tuples (or k-mers, k-grams), have been used extensively to compare genomic sequences of individual organisms, to identify cis-regulatory modules, and to study the evolution of regulatory sequences. Recently many next-generation sequencing (NGS) read data sets of metagenomic samples from a variety of different environments have been generated. The assembly of these reads can be difficult and analysis methods based on mapping reads to genes or pathways are also restricted by the availability and completeness of existing databases. Sequence-signature-based methods, however, do not need the complete genomes or existing databases and thus, can potentially be very useful for the comparison of metagenomic samples using NGS read data. Still, the applications of sequence signature methods for the comparison of metagenomic samples have not been well studied. |
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Geographical breakdown
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United States | 1 | 14% |
China | 1 | 14% |
Germany | 1 | 14% |
Unknown | 2 | 29% |
Demographic breakdown
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Members of the public | 3 | 43% |
Mendeley readers
Geographical breakdown
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Germany | 2 | 1% |
France | 2 | 1% |
Italy | 2 | 1% |
Sweden | 2 | 1% |
United Kingdom | 2 | 1% |
Austria | 1 | <1% |
South Africa | 1 | <1% |
Canada | 1 | <1% |
Other | 3 | 2% |
Unknown | 154 | 88% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 52 | 30% |
Student > Ph. D. Student | 51 | 29% |
Student > Master | 26 | 15% |
Student > Doctoral Student | 8 | 5% |
Other | 6 | 3% |
Other | 17 | 10% |
Unknown | 16 | 9% |
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Biochemistry, Genetics and Molecular Biology | 25 | 14% |
Computer Science | 17 | 10% |
Environmental Science | 4 | 2% |
Earth and Planetary Sciences | 4 | 2% |
Other | 17 | 10% |
Unknown | 20 | 11% |