extdata: Extra Data


The files in the subdirectories of extdata support the examples in the package documentation and vignettes.


Files in abundance contain protein abundance and microbial occurrence data:

Files in bison contain BLAST results and taxonomic information for a metagenome:

Files in cpetc contain heat capacity data and other thermodynamic properties:

Files in fasta contain protein sequences:

Files in protein contain protein composition data for model organisms. See more.aa and read.expr for examples that use these files.

Files in refseq contain code and results of processing NCBI Reference Sequences (RefSeq) for microbial proteins, using RefSeq release 61 of 2013-09-09:

Files in taxonomy contain example taxonomic data files:

Files in thermo contain additional thermodynamic data and group additivity definitions:


Anderson, N. L. and Anderson, N. G. (2002) The human plasma proteome: History, character and diagnostic prospects. Molecular and Cellular Proteomics 1, 845–867. http://dx.doi.org/10.1074/mcp.R200007-MCP200

Anderson, N. L. and Anderson, N. G. (2003) The human plasma proteome: History, character and diagnostic prospects (Vol. 1 (2002) 845-867). Molecular and Cellular Proteomics 2, 50. http://dx.doi.org/10.1074/mcp.A300001-MCP200

Baas Becking, L. G. M., Kaplan, I. R. and Moore, D. (1960) Limits of the natural environment in terms of pH and oxidation-reduction potentials. Journal of Geology 68(3), 243–284. http://www.jstor.org/stable/30059218

Benson, S. W. and Buss, J. H. (1958) Additivity rules for the estimation of molecular properties. Thermodynamic properties. J. Chem. Phys. 29, 546–572. http://dx.doi.org/10.1063/1.1744539

Dayhoff, M. O. and Lippincott, E. R. and Eck, R. V. (1964) Thermodynamic Equilibria In Prebiological Atmospheres. Science 146, 1461–1464. http://dx.doi.org/10.1126/science.146.3650.1461

Dayhoff, M. O. and Lippincott, E. R., Eck, R. V. and Nagarajan (1967) Thermodynamic Equilibrium In Prebiological Atmospheres of C, H, O, N, P, S, and Cl. Report SP-3040, National Aeronautics and Space Administration. http://ntrs.nasa.gov/search.jsp?R=19670017966

Dick, J. M. (2016) Proteomic indicators of oxidation and hydration state in colorectal cancer. PeerJ 4:e2238. http://dx.doi.org/10.7717/peerj.2238

Dick, J. M. and Shock, E. L. (2011) Calculation of the relative chemical stabilities of proteins as a function of temperature and redox chemistry in a hot spring. PLoS ONE 6, e22782. http://dx.doi.org/10.1371/journal.pone.0022782

Dick, J. M. and Shock, E. L. (2013) A metastable equilibrium model for the relative abundance of microbial phyla in a hot spring. PLoS ONE 8, e72395. http://dx.doi.org/10.1371/journal.pone.0072395

Domalski, E. S. and Hearing, E. D. (1993) Estimation of the thermodynamic properties of C-H-N-O-S-Halogen compounds at 298.15 K J. Phys. Chem. Ref. Data 22, 805–1159. http://dx.doi.org/10.1063/1.555927

Gattiker, A., Michoud, K., Rivoire, C., Auchincloss, A. H., Coudert, E., Lima, T., Kersey, P., Pagni, M., Sigrist, C. J. A., Lachaize, C., Veuthey, A.-L., Gasteiger, E. and Bairoch, A. (2003) Automatic annotation of microbial proteomes in Swiss-Prot. Comput. Biol. Chem. 27, 49–58. http://dx.doi.org/10.1016/S1476-9271(02)00094-4

Gaucher, E. A., Thomson, J. M., Burgan, M. F. and Benner, S. A (2003) Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature 425(6955), 285–288. http://dx.doi.org/10.1038/nature01977

Ghaemmaghami, S., Huh, W., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K. and Weissman, J. S. (2003) Global analysis of protein expression in yeast. Nature 425(6959), 737–741. http://dx.doi.org/10.1038/nature02046

Huh, W. K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S. and O'Shea, E. K. (2003) Global analysis of protein localization in budding yeast. Nature 425(6959), 686–691. http://dx.doi.org/10.1038/nature02026

HAMAP system. HAMAP FTP directory, ftp://ftp.expasy.org/databases/hamap/

Hnedkovsky, L., Wood, R. H. and Majer, V. (1996) Volumes of aqueous solutions of CH4, CO2, H2S, and NH3 at temperatures from 298.15 K to 705 K and pressures to 35 MPa. J. Chem. Thermodyn. 28, 125–142. http://dx.doi.org/10.1006/jcht.1996.0011

Hnedkovsky, L. and Wood, R. H. (1997) Apparent molar heat capacities of aqueous solutions of CH4, CO2, H2S, and NH3 at temperatures from 304 K to 704 K at a pressure of 28 MPa. J. Chem. Thermodyn. 29, 731–747. http://dx.doi.org/10.1006/jcht.1997.0192

Ishihama, Y., Schmidt, T., Rappsilber, J., Mann, M., Hartl, F. U., Kerner, M. J. and Frishman, D. (2008) Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics 9:102. http://dx.doi.org/10.1186/1471-2164-9-102

Joint Genome Institute (2007) Bison Pool Environmental Genome. Protein sequence files downloaded from IMG/M (http://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=FindGenomes&page=findGenomes)

Privalov, P. L. and Makhatadze, G. I. (1990) Heat capacity of proteins. II. Partial molar heat capacity of the unfolded polypeptide chain of proteins: Protein unfolding effects. J. Mol. Biol. 213, 385–391. http://dx.doi.org/10.1016/S0022-2836(05)80198-6

Richard, L. and Helgeson, H. C. (1998) Calculation of the thermodynamic properties at elevated temperatures and pressures of saturated and aromatic high molecular weight solid and liquid hydrocarbons in kerogen, bitumen, petroleum, and other organic matter of biogeochemical interest. Geochim. Cosmochim. Acta 62, 3591–3636. http://dx.doi.org/10.1016/S0016-7037(97)00345-1

Robie, R. A. and Hemingway, B. S. (1995) Thermodynamic Properties of Minerals and Related Substances at 298.15 K and 1 Bar (10^5 Pascals) Pressure and at Higher Temperatures. U. S. Geol. Surv., Bull. 2131, 461 p. http://www.worldcat.org/oclc/32590140

Roxby, R. and Tanford, C. (1971) Hydrogen ion titration curve of lysozyme in 6 M guanidine hydrochloride. Biochemistry 10, 3348–3352. http://dx.doi.org/10.1021/bi00794a005

SGD project. Saccharomyces Genome Database, http://www.yeastgenome.org

Shock, E. L., Oelkers, E. H., Johnson, J. W., Sverjensky, D. A. and Helgeson, H. C. (1992) Calculation of the thermodynamic properties of aqueous species at high pressures and temperatures: Effective electrostatic radii, dissociation constants and standard partial molal properties to 1000 °C and 5 kbar. J. Chem. Soc. Faraday Trans. 88, 803–826. http://dx.doi.org/10.1039/FT9928800803

Shock, E. and Canovas, P. (2010) The potential for abiotic organic synthesis and biosynthesis at seafloor hydrothermal systems. Geofluids 10, 161–192. http://dx.doi.org/10.1111/j.1468-8123.2010.00277.x

YeastGFP project. Yeast GFP Fusion Localization Database, http://yeastgfp.ucsf.edu; Current location: http://yeastgfp.yeastgenome.org

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.