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bend.it @ ICGEB Trieste, (c) 1996, A. Gabrielian, K, Vlahovicek & S. Pongor
This is a result for your query sequence "Example 1" (100 bp)
You requested a tabulated output of Bendability and Curvature propensity
Parameters:
Scale: DNaseI.sca
Window size: 30
Frequency: 36.000000 degrees
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Column 1 = Sequence
Column 2 = Bendability
Column 3 = Curvature propensity
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0 0.00 6.733e+00
1 0.00 6.600e+00
2 0.00 6.867e+00
3 0.00 7.000e+00
...
65 0.00 6.600e+00
66 0.00 6.867e+00
67 0.00 7.000e+00
68 0.00 6.733e+00
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Example 2: 1-dimensional plots
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Figure 1. Curvature propensity and bendability plot of the salivary proline-rich protein (RP-15) gene from Rattus norvegicus (Lin,H.H. and Ann,D.K.,Genomics 10:102-113, 1991, Genbank RATRP15). The profile contains one conpicuous peak of potential curvature at position 3450, which is near the 3' end of intron 2 . The magnitude of curvature propensity, 3.8 is within the range calculated for of experimentally tested curved motifs. E.g. the C.risortia bent satellite DNA has a curvature propensity value of 2.5 while the Yeast mtDNA ARS element has a value of 5.05 [Gabrielian et al, FEBS Letters, 393:124-130, 1996]. The lack of curvature is apparent in the region between 3500 and 4500, the same region has an above average bendability. This region corresponds to exon 2.
You can smooth the bendability curve for a better presentation:
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Example 3: 2-dimensional plots
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Figure 2a Curvature propensity (Y-axis) vs. bendability (X-axis) plot of the L.
tarentolae kinetoplast minicircle DNA (Genbank KILTB4MC ). The conspicuously high
curvature propensity values correspond to region 700-887. [Gabrielian et al, FEBS Letters, 393:124-130, 1996]. The consensus bendability scale
[Gabrielian and Pongor, FEBS Letters, 393:65-68, 1996] was used
with a window-length of 30 to calculate the bendability/curvature propensity values.
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Figure 2b Curvature propensity (Y-axis) vs. the G+C-content (X-axis) plot of the L. tarentolae kinetoplast minicircle DNA (Genbank KILTB4MC ). The conspicuously high curvature propensity values correspond to region 700-887 [Gabrielian et al, FEBS Letters, 393:124-130, 1996]. The G+C content of the curved motifs is an important factor, as G+C-based curvature cannot be easily predicted. The consensus bendability scale [Gabrielian and Pongor, FEBS Letters, 393:65-68, 1996] was designed to overcome this difficulty. This scale was used with a window-length of 30 to calculate the bendability/curvature propensity values.