phiX174Phage           package:Biostrings           R Documentation

_V_e_r_s_i_o_n_s _o_f _b_a_c_t_e_r_i_o_p_h_a_g_e _p_h_i_X_1_7_4 _c_o_m_p_l_e_t_e _g_e_n_o_m_e _a_n_d _s_a_m_p_l_e _s_h_o_r_t _r_e_a_d_s

_D_e_s_c_r_i_p_t_i_o_n:

     Six versions of the complete genome for bacteriophage phi X174 as
     well as a small number of Solexa short reads, qualities associated
     with those short reads, and counts for the number times those
     short reads occurred.

_D_e_t_a_i_l_s:

     The 'phiX174Phage' object is a 'DNAStringSet' containing the
     following six naturally occurring versions of the bacteriophage
     phi X174 genome cited in Smith et al.:


     _G_e_n_b_a_n_k: The version of the genome from GenBank (NC_001422.1,
          GI:9626372).

     _R_F_7_0_s: A preparation of phi X double-stranded replicative form
          (RF) of DNA by Clyde A. Hutchison III from the late 1970s.

     _S_S_7_8: A preparation of phi X virion single-stranded DNA from 1978.

     _B_u_l_l: The sequence of wild-type phi X used by Bull et al.

     _G'_9_7: The phi X replicative form (RF) of DNA from Bull et al.

     _N_E_B'_0_3: A phi X replicative form (RF) of DNA from New England
          BioLabs (NEB).  

     The 'srPhiX174' object is a 'DNAStringSet' containing short reads
     from a Solexa machine.

     The 'quPhiX174' object is a 'BStringSet' containing Solexa quality
     scores associated with 'srPhiX174'.

     The 'wtPhiX174' object is an integer vector containing counts
     associated with 'srPhiX174'.

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.genome.jp/dbget-bin/www_bget?refseq+NC_001422>

     Bull, J. J., Badgett, M. R., Wichman, H. A., Huelsenbeck, Hillis,
     D. M., Gulati, A., Ho, C. & Molineux, J. (1997) Genetics 147,
     1497-1507.

     Smith, Hamilton O.; Clyde A. Hutchison, Cynthia Pfannkoch, J.
     Craig Venter (2003-12-23). "Generating a synthetic genome by whole
     genome assembly: {phi}X174 bacteriophage from synthetic
     oligonucleotides". Proceedings of the National Academy of Sciences
     100 (26): 15440-15445. doi:10.1073/pnas.2237126100.

_E_x_a_m_p_l_e_s:

     data(phiX174Phage)
     nchar(phiX174Phage)
     genBankPhage <- phiX174Phage[[1]]
     genBankSubstring <- substring(genBankPhage, 2793-34, 2811+34)

     data(srPhiX174)
     srPhiX174
     quPhiX174
     summary(wtPhiX174)

     alignPhiX174 <-
       pairwiseAlignment(srPhiX174, genBankSubstring,
                         patternQuality = SolexaQuality(quPhiX174),
                         subjectQuality = SolexaQuality(99L),
                         type = "global-local")
     summary(alignPhiX174, weight = wtPhiX174)

