Table 1 Alignment scoring schemes used in this study, and their underlying probabilities
From: Split-alignment of genomes finds orthologies more accurately
human-chimp.v2 | HoxD70 [48] | HoxD55 | Â | Â | Â |
|---|---|---|---|---|---|
a c g t | a c g t | a c g t | Â | Â | Â |
a 90 -330 -236 -356 | a 91 -114 -31 -123 | a 91 -90 -25 -100 | Â | Â | Â |
c -330 100 -318 -236 | c -114 100 -125 -31 | c -90 100 -100 -25 | Â | Â | Â |
g -236 -318 100 -330 | g -31 -125 100 -114 | g -25 -100 100 -90 | Â | Â | Â |
t -356 -236 -330 90 | t -123 -31 -114 91 | t -100 -25 -90 91 | Â | Â | Â |
gap existence cost: 600 | gap existence cost: 400 | gap existence cost: 400 | Â | Â | Â |
gap extension cost: 150 | gap extension cost: 30 | gap extension cost: 30 | Â | Â | Â |
a c g t | a c g t | a c g t | Â | Â | Â |
a.27.00052.0020.00041 | a.18.019.045.020 | a.16.028.050.029 | Â | Â | Â |
c.00052.23.00053.0020 | c.019.16.015.045 | c.028.13.022.050 | Â | Â | Â |
g.0020.00053.23.00052 | g.045.015.16.019 | g.050.022.13.028 | Â | Â | Â |
t.00041.0020.00052.27 | t.020.045.019.18 | t.029.050.028.16 | Â | Â | Â |
gap existence probability:.000021 | gap existence probability:.043 | gap existence probability:.091 | Â | Â | Â |
gap extension probability:.11 | gap extension probability:.73 | gap extension probability:.76 | Â | Â | Â |