Images were aligned using an affine transformation to the standard MNI-152_T1 (1 mm3) template using the FSL linear registration toolkit (FLIRT) [20] with 12 degrees of freedom (alignment across 3 translations, 3 rotations, 3 scaling factors, and 3 shearing factors).
Sequences were aligned using an online version of ClustalW2 (http://www.ebi.ac.uk/Tools/msa/clustalw2/, last accessed January 8 , 2015.
An intramedullary jig was used for femoral bone cuts (5° or 7° valgus), for tibial bone cuts were aligned using an extramedullary jig.
The five highest BLASTP hits for each query sequence were aligned using an in-house Perl script to identify putative N- and/or C-termini.
After submission through this interface, each input protein is aligned using an HHsearch-based protocol against the Virfam collection of 28000 profiles generated for the present work.
For the phylogenetic analyses of our three target element superfamilies (Copia, Gypsy, and LINE), amino acid sequences belonging to each superfamily were aligned using an iterative approach.
However, the tibial cut was aligned using an external tibial reference frame and we did not detect any systematic errors, therefore, we are confident the tibial cuts were perpendicular within a few degrees as with any total knee system.
The two family alignments were aligned using a structural alignment of the two protein structures.
Prior to the adhesion measurements, the sample was aligned using a manual alignment stage and applying the alignment process published by Kroner et al. Force and displacement were recorded during all measurements.
Both reads are initially mapped separately, and if one read of the pair cannot be mapped it is aligned using a local alignment procedure (Smith-Waterman).
