Biplanar slice alignment was used.
Alignment of straightened roots was performed using the Template Matching and Slice Alignment ImageJ plugin [ 36].
Although these datasets can be used to generate highly resolved digitized 3D models of invertebrates as well (see, for example, [ 47, 48]), these analyses are extremely demanding in terms of specimen preparation, slice alignment and 3D reconstruction.
Finally, a high-resolution partial structural volume was acquired (T2*-weighted imaging, TE = 18.5 ms, TR = 680 ms, resolution 0.33 mm × 0.33 mm, 45 slices, slice thickness 1.5 mm + 25% gap, FOV 212 mm × 179 mm, matrix 640 × 540), with a slice alignment orthogonal to the hippocampus main axis.
23, 53 From a different point of view, the reads that locate at the exon intron boundaries are helps with the determination of the alternative splicing pattern, where advent RNA-seq promotes the development of new generation of slice-alignment software such as BLAT, 54, 55 TopHat, 56, 57 GEM, 58 and MapSplice.
Data were preprocessed using the Duke BIAC resting state pipeline based on the tools from the FSL analysis package (FMRIB Software Library, http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/, Version 5.98) and locally developed MATLAB code (MathWorks, Natick, MA), including slice-timing alignment, motion correction, coregistration, nonbrain voxel extraction, and normalization.
In addition to several cleaning steps, which are described in the RNAz manual [ 72], the rnazWindows.pl tool sliced the alignments in 40 nt overlapping windows of size 120.
For each SNP within an aligned region, two allelic versions of a 110-bp alignment slice centered around the SNP were searched for putative TFBS using the TFBS Perl modules [ 33] and all position-weight matrices in the JASPAR database describing vertebrate TFBS and having an information content of at least 7 [ 27].
Numerous technical challenges must be addressed to obtain consistent vital cardiac slices with uniform thickness and minimal tissue damage, including slow vibratome blade advance speeds (50 μm/s or less), minimal z-axis blade deflection (<1 μm), slice thicknesses, and alignment of the cutting plane.
RNAz was applied to the filtered input alignment slices in both reading directions.
In a series of filtering steps, sequences were removed from the individual alignments or alignment slices if they are (a) shorter than 50 nt, or (b) contain more than 25% gap characters, or (c) have a base composition outside the definition range of RNAz (e.g. GC content > 0.75 or < 0.25).
