phiX174Phage {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
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)