Community-wide analysis of microbial genome sequence signatures

doi:10.1186/gb-2009-10-8-r85

Genome Biology

Volume 10
Issue 8

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Dick GJ
Andersson AF
Baker BJ
Simmons SL
Thomas BC
Yelton AP
Banfield JF

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Simmons SL
Thomas BC
Yelton AP
Banfield JF
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Community-wide analysis of microbial genome sequence signatures

Gregory J Dick¹^,3 , Anders F Andersson¹^,4^,5 , Brett J Baker¹ , Sheri L Simmons¹ , Brian C Thomas¹ , A Pepper Yelton¹ and Jillian F Banfield¹^,2

¹Department of Earth and Planetary Science, University of California, 307 McCone Hall, Berkeley, CA 94720, USA

²Department of Environmental Science, Policy, and Management, University of California, Hilgard Hall, Berkeley, CA 94720, USA

³Current address: Department of Geological Sciences, University of Michigan, 1100 N. University Ave, Ann Arbor, MI 48109-1005, USA

⁴Current address: Evolutionary Biology Centre, Department of Limnology, Uppsala University, Norbyv. 18 D, SE-75236, Uppsala, Sweden

⁵Current address: Department of Bacteriology, Swedish Institute for Infectious Disease Control, Nobels väg 18 SE-17182 Solna, Sweden

author email corresponding author email

Genome Biology 2009, 10:R85doi:10.1186/gb-2009-10-8-r85


Published:	21 August 2009

Subject areas: Bioinformatics, Ecology, Genome studies

Additional files

Additional File 1:

Automated clustering of tetra-ESOM data using fixed point kernel densities.

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Additional File 2:

Evaluation of binning accuracy based on deeply sampled metagenomes for which contigs are assigned to genomes with a high degree of confidence.

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Additional File 3:

Binning accuracy calculated for genomes that were sampled to varying extents of completeness (10 to 100%).

Format: PDF Size: 145KB Download file

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Additional File 4:

Heat map of average genome-wide frequency of each tetranucleotide for each genome, including bacteria, archaea, viruses, and a putative plasmid.

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Additional File 5:

Comparison of tetra-ESOMs of assembled genomes based on (a) amino acid composition, (b) codon composition, and (c) tetranucleotide frequency

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Additional File 6:

The observed difference in frequency of each tetranucleotide between pairs of genomes correlates with the difference predicted based on codon composition.

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Additional File 7:

Tetra-ESOM of deeply sampled genomes for which coding and noncoding regions were separated.

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Additional File 8:

Percentage of sequence coding for genes in comparison with the genome-wide coding percentage for incorrectly binned fragments.

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Additional File 9:

Tetra-ESOM of Leptospirillum group II genes coding for highly expressed proteins or proteins enriched in the extracellular fraction analyzed as separate fractions from the rest of the genome.

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Additional File 10:

Processes and factors influencing genome signature.

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