Versions of bacteriophage phiX174 complete genome and sample short reads
Six versions of the complete genome for bacteriophage φ 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.
The phiX174Phage object is a DNAStringSet containing the
following six naturally occurring versions of the bacteriophage φ X174
genome cited in Smith et al.:
The version of the genome from GenBank (NC\_001422.1, GI:9626372).
A preparation of φ X double-stranded replicative form (RF) of DNA by Clyde A. Hutchison III from the late 1970s.
A preparation of φ X virion single-stranded DNA from 1978.
The sequence of wild-type φ X used by Bull et al.
The φ X replicative form (RF) of DNA from Bull et al.
A φ 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.
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.
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.