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Bioinformatics Journal (Oxford Academia) (genomic features can predict…
Bioinformatics Journal (Oxford Academia)
genomic features can predict growth temperature in bacteria (Sauer and Wang, 2019)
Points
corelation between OGT and G+C mRNA content (Hurst and Merchant, 2001)
cor. between the charged versus polar
amino acid ratios(Suhre and Claverie, 2003)
Methods
tRNA, rRNA, ORF sequences from Ensembl Bacteria (Kersey et al.,
2016)
tRNAScan-SE 2.0 (Lowe and Chan, 2016)
Barrnap 0.9(rRNA)
using hidden Markov models
BEDtools 2.27.1 (Quinlan and Hall, 2010) (rRNA)
Prodigal 2.6.3 (Hyatt et al., 2010) (ORF)
Calculating features per basis per species
Pearson cor. coef (r) between OGT and genome feature value
Dataset generation
species were randomly assigned to training and test dataset (holdout method for cross validation)
Multiple linear regression
(quantitative genomic, tRNA, rRNA, ORF, proteom features) (only for those that r>0.3) ~ OGT
Species distance comparison
using Biopython Phylo library accessing to All-Species Living Tree
project’s SSU rRNA tree (Yarza et al., 2008)
Software
NumPy 1.15.1 (van der Walt et al.,
2011)
SciPy 1.1.0, Scikit-learn 0.19.2 (Pedregosa et al., 2011)
Biopython 1.72 (Cock et al., 2009)
MatPlotLib 2.2.3 (Hunter, 2007)
Results
negative correlation between genome size and OGT's species
proteome had strong correlatoion with OTG's species