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There was no relation between the alignment percentage and tumor response (Figure 5), signal to noise ratio of either the liver or normal parts of the lung, or with the distribution of the original SUV. Figure 5 Relation between thoracic imaging alignment and tumor response according to RECIST criteria per patient.

On average, the alignment percentage and root-mean-square distance (RMSD) computed by the proposed method were 90% and 1.8Å for a set of 1,211 DS-related pairs of proteins.

On average, the alignment percentage and root-mean-square distance (RMSD) computed by the proposed method were 90% and 1.8Å for a set of 1,211 DS-related pairs of proteins, which is the largest DS dataset available.

Secondly, we improved the classical all-versus-all BLASTP [ 23] approach to identifying pairs of best reciprocal hits (BRH) [ 24] with a dedicated Perl script, enhancing the definition of orthologs by specifying two parameters, the alignment percentage and the score ratio, to filter the BLAST results.

Longer tag sequences, higher alignment percentages and more stringent gap and mismatch scores will result in more accurate tag sequence identification.

Table 1 Alignment percentage per patient between elastix and baseline image of intra- and extra-thoracic measurable lesions Pts       Thoracic Extra-thoracic   Age Sex RECIST N % ΔSUV %Δ perc.

Trimming 4 bp and 9 bp from 5′ end resulted in a larger improvement in alignment percentages (84 and 89%, respectively), which is likely the result of removing low quality information from the reads.

The alignment percentage per patient using ΔSUV and Δ percentage is detailed in Table 2.

Alignments were then extracted and filtered by the length of the sequence overlap (minimum of 100 bp) and the average alignment percentage identity (minimum of 75%).

A typical alignment percentage defined as number of uniquely aligned reads over total pass filtered reads was around 55-65%.

Phylogenetic analysis was further confirmed by the multiple alignment percentage identity of 76.06% among their residues by using ClustalW and T-Coffee along with rapid scanning and correction of multiple sequence alignments).