References
- Sanger, F. and A. R. Coulson (1975) A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J. Mol. Biol. 94: 441-446. https://doi.org/10.1016/0022-2836(75)90213-2
- Sanger, F., S. Nicklen, and A. R. Coulson (1977) DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. U.S.A. 74: 5463-5467. https://doi.org/10.1073/pnas.74.12.5463
- Sorek, R., Y. Zhu, C. J. Creevey, M. P. Francino, P. Bork, and E. M. Rubin (2007) Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer. Science 318: 1449-1452. https://doi.org/10.1126/science.1147112
- Picardi, E. and G. Pesole (2010) Computational Methods for Ab Initio and Comparative Gene Finding. pp. 269-284 In: Carugo, O., and F. Eisenhaber (eds.). Data Mining Techniques for the Life Science. Humana Press, New York.
- Pinard, R., A. de Winter, G. Sarkis, M. Gerstein, K. Tartaro, R. Plant, M. Egholm, J. Rothberg, and J. Leamon (2006) Assessment of whole genome amplificationinduced bias through high-throughput, massively parallel whole genome sequencing. BMC Genomics. 7: 216. https://doi.org/10.1186/1471-2164-7-216
- Handelsman, J., M. R. Rondon, S. F. Brady, J. Clardy, and R. M. Goodman (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem. Biol. 5: R245-R249. https://doi.org/10.1016/S1074-5521(98)90108-9
- Batzoglou, S., D. B. Jaffe, K. Stanley, J. Butler, S. Gnerre, E. Mauceli, B. Berger, J. P. Mesirov, and E. S. Lander (2002) ARACHNE: A Whole-Genome Shotgun Assembler. Genome Res. 12: 177-189. https://doi.org/10.1101/gr.208902
- Aparicio, S., J. Chapman, E. Stupka, N. Putnam, J.-m. Chia, P. Dehal, A. Christoffels, S. Rash, S. Hoon, A. Smit, M. D. S. Gelpke, J. Roach, T. Oh, I. Y. Ho, M. Wong, C. Detter, F. Verhoef, P. Predki, A. Tay, S. Lucas, P. Richardson, S. F. Smith, M. S. Clark, Y. J. K. Edwards, N. Doggett, A. Zharkikh, S. V. Tavtigian, D. Pruss, M. Barnstead, C. Evans, H. Baden, J. Powell, G. Glusman, L. Rowen, L. Hood, Y. H. Tan, G. Elgar, T. Hawkins, B. Venkatesh, D. Rokhsar, and S. Brenner (2002) Whole- Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes. Science 297: 1301-1310. https://doi.org/10.1126/science.1072104
- Myers, E. W., G. G. Sutton, A. L. Delcher, I. M. Dew, D. P. Fasulo, M. J. Flanigan, S. A. Kravitz, C. M. Mobarry, K. H. Reinert, nbsp, J., K. A. Remington, E. L. Anson, R. A. Bolanos, H.-H. Chou, C. M. Jordan, A. L. Halpern, S. Lonardi, E. M. Beasley, R. C. Brandon, L. Chen, P. J. Dunn, Z. Lai, Y. Liang, D. R. Nusskern, M. Zhan, Q. Zhang, X. Zheng, G. M. Rubin, M. D. Adams, and J. C. Venter (2000) A Whole-Genome Assembly of Drosophila. Science 287: 2196-2204. https://doi.org/10.1126/science.287.5461.2196
- Chaisson, M. J. and P. A. Pevzner (2008) Short read fragment assembly of bacterial genomes. Genome Res. 18: 324-330. https://doi.org/10.1101/gr.7088808
- Pevzner, P. A., H. Tang, and M. S. Waterman (2001) An Eulerian path approach to DNA fragment assembly. Proc. Natl. Acad. Sci. USA. 98: 9748-9753. https://doi.org/10.1073/pnas.171285098
- Mavromatis, K., N. Ivanova, K. Barry, H. Shapiro, E. Goltsman, A. C. McHardy, I. Rigoutsos, A. Salamov, F. Korzeniewski, M. Land, A. Lapidus, I. Grigoriev, P. Richardson, P. Hugenholtz, and N. C. Kyrpides (2007) Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat. Meth. 4: 495-500. https://doi.org/10.1038/nmeth1043
- Altschul, S., T. Madden, A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. Lipman (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25: 3389-3402. https://doi.org/10.1093/nar/25.17.3389
- Azad, R. K. and M. Borodovsky (2004) Probabilistic methods of identifying genes in prokaryotic genomes: Connections to the HMM theory. Brief. Bioinformatics 5: 118-130. https://doi.org/10.1093/bib/5.2.118
- Yooseph, S., W. Li, and G. Sutton (2008) Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering. BMC Bioinformatics 9: 182. https://doi.org/10.1186/1471-2105-9-182
- Yooseph, S., G. Sutton, D. B. Rusch, A. L. Halpern, S. J. Williamson, K. Remington, J. A. Eisen, K. B. Heidelberg, G. Manning, W. Li, L. Jaroszewski, P. Cieplak, C. S. Miller, H. Li, S. T. Mashiyama, M. P. Joachimiak, C. van Belle, J.-M. Chandonia, D. A. Soergel, Y. Zhai, K. Natarajan, S. Lee, B. J. Raphael, V. Bafna, R. Friedman, S. E. Brenner, A. Godzik, D. Eisenberg, J. E. Dixon, S. S. Taylor, R. L. Strausberg, M. Frazier, and J. C. Venter (2007) The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families. PLoS Biol. 5: e16. https://doi.org/10.1371/journal.pbio.0050016
- Epshtein, V., D. Dutta, J. Wade, and E. Nudler (2010) An allosteric mechanism of Rho-dependent transcription termination. Nature 463: 245-249. https://doi.org/10.1038/nature08669
- Salis, H. M., E. A. Mirsky, and C. A. Voigt (2009) Automated design of synthetic ribosome binding sites to control protein expression. Nat. Biotechnol. 27: 946-950. https://doi.org/10.1038/nbt.1568
- Koo, B. M., V. A. Rhodius, G. Nonaka, P. L. deHaseth, and C. A. Gross (2009) Reduced capacity of alternative sigmas to melt promoters ensures stringent promoter recognition. Genes Dev. 23: 2426-2436. https://doi.org/10.1101/gad.1843709
- Young, B. A., T. M. Gruber, and C. A. Gross (2004) Minimal machinery of RNA polymerase holoenzyme sufficient for promoter melting. Science 303: 1382-1384. https://doi.org/10.1126/science.1092462
- Huerta, A. M. and J. Collado-Vides (2003) Sigma70 Promoters in Escherichia coli: Specific Transcription in Dense Regions of Overlapping Promoter-like Signals. J. Mol. Biol. 333: 261-278. https://doi.org/10.1016/j.jmb.2003.07.017
- Venter, J. C., K. Remington, J. F. Heidelberg, A. L. Halpern, D. Rusch, J. A. Eisen, D. Wu, I. Paulsen, K. E. Nelson, W. Nelson, D. E. Fouts, S. Levy, A. H. Knap, M. W. Lomas, K. Nealson, O. White, J. Peterson, J. Hoffman, R. Parsons, H. Baden-Tillson, C. Pfannkoch, Y.-H. Rogers, and H. O. Smith (2004) Environmental Genome Shotgun Sequencing of the Sargasso Sea. Science 304: 66-74. https://doi.org/10.1126/science.1093857
- Rusch, D. B., A. L. Halpern, G. Sutton, K. B. Heidelberg, S. Williamson, S. Yooseph, D. Wu, J. A. Eisen, J. M. Hoffman, K. Remington, K. Beeson,B. Tran, H. Smith, H. Baden-Tillson, C. Stewart, J. Thorpe, J. Freeman, C. Andrews-Pfannkoch, J. E. Venter, K. Li, S. Kravitz, J. F. Heidelberg, T. Utterback, Y.-H. Rogers, L. I. Falcón, V. Souza, G. Bonilla-Rosso, L. E. Eguiarte, D. M. Karl, S. Sathyendranath, T. Platt, E. Bermingham, V. Gallardo, G. Tamayo-Castillo, M. R. Ferrari, R. L. Strausberg, K. Nealson, R. Friedman, M. Frazier, and J. C. Venter (2007) The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol. 5: e77. https://doi.org/10.1371/journal.pbio.0050077
- Walsh, D. A., E. Zaikova, C. G. Howes, Y. C. Song, J. J. Wright, S. G. Tringe, P. D. Tortell, and S. J. Hallam (2009) Metagenome of a Versatile Chemolithoautotroph from Expanding Oceanic Dead Zones. Science 326: 578-582. https://doi.org/10.1126/science.1175309
- Kanhere, A. and M. Bansal (2005) A novel method for prokaryotic promoter prediction based on DNA stability. BMC Bioinformatics 6: 1. https://doi.org/10.1186/1471-2105-6-1
- Reese, M. G. (2001) Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput. Chem. 26: 51-56. https://doi.org/10.1016/S0097-8485(01)00099-7
- Galperin, M. Y. and E. V. Koonin (2010) From complete genome sequence to 'complete' understanding? Trends Biotechnol. 28: 398-406. https://doi.org/10.1016/j.tibtech.2010.05.006
- Whitman, W. B., D. C. Coleman, and W. J. Wiebe (1998) Prokaryotes: The unseen majority. Proc. Natl. Acad. Sci. USA. 95: 6578-6583. https://doi.org/10.1073/pnas.95.12.6578