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The minimum distance between ROIs and surrounding tissue layer boundaries was determined using the intrinsic MATLAB function dist.
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By means of stochastic transformations of state norm process, the stability boundaries are determined using the stochastic averaging method and a technique due to Khasminskii.
Aligned ORF boundaries were determined using the GenBank files as guides and confirmed by visual inspection of the alignments.
For a select subset of SMC proteins, coiled coil boundaries were determined using other coiled coil prediction software including PairCoil2 ([50]; http://groups.csail.mit.edu/cb/paircoil2/) and PCOILS ([51]; http://toolkit.tuebingen.mpg.de/pcoils).
Initially, repeat boundaries were determined using RepeatMasker.
Block boundaries were determined using the criterion of Gabriel et al (2002).
Consensus exon/intron boundaries were determined using wheat EST sequences aligned to the genomic sequence.
These exons were verified by RT-PCR and the intron-exon boundaries were determined using intron-spanning PCRs on genomic DNA followed by Sanger sequencing.
Analytical results for the phase boundaries were determined using asymptotic expansions and linear stability analysis (see Additional file 1: Section 2 for details).
The intron/exon boundaries were determined using Spidey (http://www.ncbi.nlm.nih.gov/spidey/) and Softberry FGENESH (http://linux1.softberry.com/all.htm) software and by manual sequence analysis using Geneious v5.5 (Biomatters Ltd).
The position of the boundary was determined using topography data from 135 × 135 μm2 scan.
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