The score is adjusted by subtracting the initial score s init which is defined as the last minimal score encountered during traceback before the score exceeds the final alignment score or 0 if no such minimum exists.
A minimum score of 250, corresponding to a minimal alignment length of 50 bp, was applied following the usual recommendations to map orthologous ESTs [ 29].
Program parameters were varied in repeated runs: CYNTENATOR gap and mismatch penalty parameters were set to 0.1, 0.5, 1, 2, 3, 5, 20, the alignment score threshold was set to 1, the minimal alignment length to 2, the maximal number of retained alignments to 1,000 and the gene coverage filter to 4. MCMuSeC was run to report gene clusters, which are shared by at least two genomes.
BEAMS [ 14] is another recent multiple network alignment algorithm, which first extracts the so-called "backbones", or the minimal set of disjoint cliques in the filtered similarity graph, and then iteratively merges these backbones to maximize the overall alignment score.
Z-score indicates how many standard deviations the current alignment score differs from the average Z-score, calculated from all binding sites alignments over the entire PDB [19].
Improvement of alignment is evaluated by to two metrics known as morphology alignment score and correlation coefficient.
Furthermore, minimal alignment length (hsp filter) was set to 33 to avoid hits with matching region smaller than 100 nucleotides.
Alignment candidate threshold (minimal alignment length to map the read) was optimized with hash size 20.
Each comparison yielded an alignment score.
For read mapping, the minimal read coverage was set at 90% and the minimal alignment identity at 90%.
