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The individual reads were then screened for known repetitive elements and repeat masked using the cGRASP RepeatMasker database http://lucy.ceh.uvic.ca/repeatmasker/cbr_repeatmasker.py and sequences with at least 50 consecutive non-repetitive bases were mapped onto the assembly using ssaha2[ 32].
Specifically, the use of the partial proportional formulation allows a much better identification of the increasing effect of alcohol and/or drug use on crash injury severity, which previously was masked using the conventional ordered probability models.
WM images were exclusively masked using the same mask to avoid overlaps between GM and WM voxels due to smoothing.
For this reason, all voxels belonging to WM were masked using the ImCalc function in the SPM5 software package by filtering this specific intensity in the whole image.
Repeats within the cleaned ESTs were masked using the online service RepeatMasker (version 3.2.6, RM-20080801, Smit et al., unpublished data) followed by a second Seqclean run to eliminate low quality and short sequences.
Ocean pixels in all output layers were masked using the MODLAND Digital Elevation Model (DEM) and Land/Water Mask version 4, downloaded from ftp://landsc1.nascom.nasa.gov/pub/outgoing/dem_sin_old for all 229 tiles and processed in ERDAS Imagine 9.0 and ArcInfo 9.1 (ESRI, Redlands, CA).
Indeed, masking using the MIPS REcat library, resulted in a total repeat coverage of 80.8% (range 36.8 100.0% on individual clones).
The genomic sequence of E. coli was also masked using cross_match (with the parameters: -minmatch 100 -minscore 150).
Target sequences were also repeat masked using RepeatMasker and the primate repeat database obtained from Repbase [ 33].
Air was masked using a signal threshold on the short echo images.
Raw images were linearly brightened, rescaled and linearly filtered by a subresolution mask using the image processing program ImageJ (Wayne Rasband, US National Institutes of Health, [ 51]).
