References

The development and interpretation of this pipeline were influenced by foundational research in genomics and hydropathy analysis:

  1. Galtier, N. & Lobry, J.R. (1997). "Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes." J Mol Evol, 44(6): 632–636.

  2. Hurst, L.D. & Merchant, A.R. (2001). "High guanine–cytosine content is not an adaptation to high temperature: a comparative analysis amongst prokaryotes." Proc. R. Soc. B, 268(1466): 493–497.

  3. Ilatovskiy, A., Petukhov, M. "Genome-wide search for local DNA segments with anomalous GC-content."

  4. Kyte, J. & Doolittle, R.F. (1982). "A simple method for displaying the hydropathic character of a protein." J Mol Biol, 157(1): 105–132.

  5. Makino, K., et al. (1999). "Complete nucleotide sequence of the prophage VT2-Sakai..." Genes Genet Syst, 74(5): 227–239.

  6. Welch, R.A., et al. (2002). "Extensive mosaic structure revealed by the complete genome sequence of uropathogenic E. coli." Proc. Natl. Acad. Sci. USA, 99(26): 17020–17024.

  7. Šmarda, P., et al. (2014). "Genomic GC content diversity in monocots." Proc. Natl. Acad. Sci., 111(39): E4096–E4102.

  8. Yakovchuk, P., et al. (2006). "Base-stacking and base-pairing contributions into thermal stability of the DNA double helix." Nucleic Acids Res, 34(2): 564–574.

  9. Jamison, C. (2004). Perl Programming for Bioinformatics & Biologists, Wiley DreamTech.

  10. Moorhouse, M., et al. (2004). Bioinformatics, Biocomputing and PERL, Wiley & Sons.

  11. Dwyer, R.A. (2003). Genomic Perl: From Bioinformatics Basics to Working Code, Cambridge University Press.

  12. Mölder F, Jablonski KP, Letcher B et al. Sustainable data analysis with Snakemake [version 1; peer review: 1 approved, 1 approved with reservations]. F1000Research 2021, 10:33 (https://doi.org/10.12688/f1000research.29032.1)