PCA-based linear combinations of oligonucleotide frequencies for metagenomic DNA fragment binning

@article{Wu2008PCAbasedLC,
  title={PCA-based linear combinations of oligonucleotide frequencies for metagenomic DNA fragment binning},
  author={Hongwei Wu},
  journal={2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology},
  year={2008},
  pages={46-53}
}
In this paper we have investigated linear combinations of oligonucleotide (k-mer) frequencies for binning the metagenomic DNA fragments of short-to-moderate lengths. The k-mer frequencies have been widely used for gene prediction, phylogenetic tree construction, and metagenomic binning. However, the k-mer frequencies will lead to a high dimensional feature space even for a modest value of k. Existing methods to reduce the dimensionality of the feature space focus on particular oligonucleotide… CONTINUE READING

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2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology • 2009
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References

Publications referenced by this paper.
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Viral metagenomics

Nature Reviews Microbiology • 2005

Metagenomics: application of genomics to uncultured microorganisms.

Microbiology and molecular biology reviews : MMBR • 2004

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