Given two sequences with a homolog in PDB, one can accurately superpose the PDB structures (templates) and map the resulting alignment onto the original sequences.
We built a PRAME protein homology model using the PRAME gene on BTA16 (GenBank acc. no. XM_001256020) as the template, and mapped the positively selected sites on the model (Fig. 5).
First, the ARM approach is introduced in detail, including archetype modelling, template definition, and mapping rules.
In the method from [ 13], the CT template is directly registered to the patient MRI image while in other methods [ 14– 17], an MRI image is associated with the μ-map template and the mapping is performed between the template and patient MRI images.
DNA templates and genetic map data from the interspecific Allium cross A. cepa × A. roylei were used as described by Van Heusden et al. (2000a, b).
Three XML formats are used for the different elements in our approach: content sequences, templates and the resulting mapping of content of a sequence into page templates.
Note that the matching network also mirrors the translation-invariant mapping of the bottom-up pathway by implementing the comparison between matching template and feature maps in a location-by-location fashion.
An optimized method of VBM was applied using both customized templates and prior probability maps, implemented using SPM5.
An optimized method of voxel-based morphometry was applied using both customized templates and prior probability maps (Senjem et al., 2005), implemented using SPM5 (http://www.fil.ion.ucl.ac.uk/spm).ac.uk/spm
In our examples we have chosen proteins that can be modelled from highly homologous templates and which have mapped epitopes (enolases, subtilisin type proteases and ribotoxin), these are shown in figures 5, 6 and 7 and described in the following 8 paragraphs.
