# HG changeset patch
# User bgruening
# Date 1393073812 18000
# Node ID 412a7b592d7bb0abdf20820e0deb9c4599ab43bd
initial Uploaded
diff -r 000000000000 -r 412a7b592d7b tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Sat Feb 22 07:56:52 2014 -0500
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+ http://www.cbp.ens-lyon.fr/lib/exe/fetch.php?media=developpement:productions:logiciels:twist-dna_1.1.tar.gz
+ make
+ $INSTALL_DIR/bin
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+ TwistDNA
+ $INSTALL_DIR/bin
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+ $INSTALL_DIR/bin
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+ Compiling TwistDNA requires a C compiler and gfortran (typically gcc)
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diff -r 000000000000 -r 412a7b592d7b twistdna.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/twistdna.xml Sat Feb 22 07:56:52 2014 -0500
@@ -0,0 +1,72 @@
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+ Twist-DNA allows visualization of results in standard genome browsers to compare DNA opening properties to other available datasets
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+ twistdna
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+cp $configfile "input.dat";
+mkdir param;
+mkdir outputs;
+cp $enthalpy "param/param_enthalpy.dat";
+cp $entropy "param/param_entropy.dat";
+TwistDNA < $input;
+##remove the first line, because there they are useless
+tail -n+2 outputs/bubblethresh.bed | tr -s ' ' '\t' > $outfile1;
+tail -n+2 outputs/openproba.bed | tr -s ' ' '\t' > $outfile2;
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+$getVar('check.temperature', '37') ::Temperature T in Celsius (default 37 C)
+$getVar('check.sigma', '-0.06') ::Superhelical density Sigma (default -0.06)
+$getVar('check.salt', '0.1') ::Salt concentration CNa (default 0.1 M)
+$getVar('check.small_bubble', '1') ::Smallest bubble size bsizemin
+$getVar('check.large_bubble', '0') ::Largest bubble size bsizemax
+$getVar('check.bubble_size_step', '1') ::Bubble size step bstep
+$getVar('check.threshold', '-3.0') ::Bubble storing threshold (default -3)
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+
+-12.84 -12.52 -11.58 -13.72
+-13.43 -13.00 -13.72 -15.89
+-11.72 -13.67 -12.84 -13.43
+-13.67 -17.07 -12.52 -13.00
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+-11.29 -10.53 -10.16 -11.56
+-11.38 -9.89 -11.56 -12.42
+-10.89 -11.55 -11.29 -11.38
+-11.55 -13.68 -10.53 -9.89
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+ **What it does**
+ http://www.cbp.ens-lyon.fr/doku.php?id=developpement:productions:logiciels:twistdna
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+ Local opening of the DNA double-helix is required in many fundamental biological processes and is in part controlled by the degree of superhelicity imposed in vivo by the protein machinery. In particular, positions of superhelically destabilized regions correlate with regulatory sites along the genome. Based on a self-consistent linearization of a thermodynamic model of superhelical DNA introduced by Benham, we have developed Twist-DNA, a program that predicts the locations of these regions by efficiently computing base-pair and bubble opening probabilities in genomic DNA. The program allows visualization of results in standard genome browsers to compare DNA opening properties to other available datasets.
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