phiX174Phage           package:Biostrings           R Documentation

Versions of bacteriophage phiX174 complete genome and sample short reads

Description:

     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.

Details:

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


     Genbank: The version of the genome from GenBank (NC_001422.1,
          GI:9626372).

     RF70s: A preparation of phi X double-stranded replicative form
          (RF) of DNA by Clyde A. Hutchison III from the late 1970s.

     SS78: A preparation of phi X virion single-stranded DNA from 1978.

     Bull: The sequence of wild-type phi X used by Bull et al.

     G'97: The phi X replicative form (RF) of DNA from Bull et al.

     NEB'03: 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'.

References:

     <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.

Examples:

     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)

