view release on metacpan or  search on metacpan

t/data/demos/12169614.utf8  view on Meta::CPAN

were averaged and treated as a single value for the experiment. The
ratios from the independent samples were log transformed, and then
the data for each individual spot were averaged between the replicate
experiments. We then calculated the geometric mean and standard
deviation of the entire population. Any spot that had a ratio that was
more than 2.5 standard deviations away from the mean was considered an
outlier. Outliers were then removed from the population, and the means
and standard deviations were recalculated. Once again, any spot more
than 2.5 standard deviations away from the mean was considered an
outlier. This process was repeated until few or no outliers were
detected. In these experiments generally three iterations were needed
to identify all outliers in the population.
Array data were also analyzed with the Rosetta Resolver application
Axon error model (Rosetta Biosoftware). The lists of outliers from the
two analysis methods were compared, and only those genes that were
considered significantly changed in both were considered further. The
range of ratios of the outliers was from a high of 12 to a low of 1.6.
HMM analysis.
The sigma-H promoter sequence was modeled by using the HMMER 2.1.1
suite of software packages to create a series of closely related HMMs
(http://hmmer.wustl.edu). Known sigma-H promoter sequences from

t/data/good/10862768.utf8  view on Meta::CPAN

   structure factor amplitudes of solvent molecules in the crystal were
   calculated using the bulk solvent correction routine in XPLOR ([70]19),
   and thus the low resolution limit could be extended to 50.0 Ã…
   resolution. Crystallographic refinement including simulated annealing,
   conjugate gradient minimization, and individual B-factor refinement was
   then performed at the resolution between 50.0 and 2.5 Ã…. After the
   first round of refinement, the quality of the structure was
   dramatically improved with a working R factor of 27.4% and a freeR
   factor of 30.1%. The F [o] −F [c] difference map showed continuous
   density for CoA, verifying the correct molecular replacement solution.
   Several iterations of model building in the program O ([71]17) and the
   refinement in the program XPLOR ([72]19) further dropped both R
   factors. The final refinement statistics are shown in Table [73]II.
   Because of the slight difference between four subunits,
   noncrystallographic symmetry restraints were applied to only 89% of
   total residues of each subunit. In the final model, residues 1–5 in
   subunit 1; residues 1–7 and 211–212 in subunit 2; residues 1–5 and
   210–213 in subunit 3; and residues 1–7, 83–85, and 212–214 in subunit 4
   are excluded because they are disordered in the crystal.
   [74]Previous Section[75]Next Section