# HG changeset patch
# User bgruening
# Date 1389707423 18000
# Node ID f486cceb3a80f4d17d75522529fba885751664fb
Uploaded
diff -r 000000000000 -r f486cceb3a80 rnaz.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaz.xml Tue Jan 14 08:50:23 2014 -0500
@@ -0,0 +1,49 @@
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+ predicting structurally conserved and thermodynamically stable RNA secondary structures
+ RNAz --version
+
+ rnaz
+
+
+RNAz $input
+$forward
+$reverse
+$both_strands
+$dinucleotide
+$mononucleotide
+$locarnate
+$no_shuffle
+#if $cutoff_p != -1:
+--cutoff=$cutoff_p
+#end if
+> temp.txt;
+grep -v -E "^ |^#|^$" temp.txt > $outfile;
+grep -E "^ |^#|^$" temp.txt;
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+ **What it does**
+ RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. It can be used in genome wide screens to detect functional RNA structures, as found in noncoding RNAs and cis-acting regulatory elements of mRNAs.
+
+
+Gruber AR, Findeiss, Washietl S, Hofacker IL, and Stadler PF.
+RNAz 2.0: Improved noncoding rna detection.
+Pac Symp Biocomput, 2010. 15:69–79.
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+
diff -r 000000000000 -r f486cceb3a80 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue Jan 14 08:50:23 2014 -0500
@@ -0,0 +1,14 @@
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+ http://www.tbi.univie.ac.at/~wash/RNAz/RNAz-2.1.tar.gz
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+ $INSTALL_DIR/bin
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+ Compiling RNAz requires a C compiler (typically gcc)
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+