# HG changeset patch
# User bernhardlutz
# Date 1389732513 18000
# Node ID 93a6f5eb2f9a10825a8ee8e4c65e5b66c359ee02
Uploaded
diff -r 000000000000 -r 93a6f5eb2f9a intarna.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/intarna.xml Tue Jan 14 15:48:33 2014 -0500
@@ -0,0 +1,40 @@
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+ intarna
+ vienna_rna
+
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+IntaRNA
+-m $query_file
+-t target_file
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+ **What it does**
+IntaRNA is a program for the fast and accurate prediction of interactions between two RNA molecules. It has been designed to predict mRNA target sites for given non-coding RNAs (ncRNAs) like eukaryotic microRNAs (miRNAs) or bacterial small RNAs (sRNAs), but it can also be used to predict other types of RNA-RNA interactions.
+
+Anke Busch, Andreas S. Richter, and Rolf Backofen
+IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
+Bioinformatics, 24 no. 24 pp. 2849-56, 2008
+Andreas S. Richter, Christian Schleberger, Rolf Backofen, and Claudia Steglich
+Seed-based IntaRNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1
+Bioinformatics, 26 no. 1 pp. 1-5, 2010
+
+**Output**
+
+
diff -r 000000000000 -r 93a6f5eb2f9a test-data/example.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.fasta Tue Jan 14 15:48:33 2014 -0500
@@ -0,0 +1,4 @@
+>ncRNA1
+AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU
+>ncRNA2
+ACUGAGGUACGAUCGUGGCAGGGCCUUUGACUGACUUUCGUACUUU
diff -r 000000000000 -r 93a6f5eb2f9a test-data/example.fasta~
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.fasta~ Tue Jan 14 15:48:33 2014 -0500
@@ -0,0 +1,4 @@
+>ncRNA1
+AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU
+>ncRNA2
+ACUGAGGUACGAUCGUGGCAGGGCCUUUGACUGACUUUCGUACUUU
diff -r 000000000000 -r 93a6f5eb2f9a test-data/example2.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example2.fasta Tue Jan 14 15:48:33 2014 -0500
@@ -0,0 +1,8 @@
+>mRNA1
+UUUAAAUUAAAAAAUCAUAGAAAAAGUAUCGUUUGAUACUUGUGAUUAUACUCAGUUAUA
+CAGUAUCUUAAGGUGUUAUUAAUAGUGGUGAGGAGAAUUUAUGAAGCUUUUCAAAAGCUU
+GCUUGUGGCACCUGCAACUCUUGGUCUUUUAGCACCAAUGACCGCUACUGCUAAU
+>mRNA2
+UGCUUCUUAGUAAUGGCCAGCUCGGGGAUUUGGAACUGGUGGUUGUUAAUUCUAGGCAAA
+UAGAUUAAAAUUAAAUUACUCAAAUUGUGUGACGAGUUUUAUGAAGCUUUUUAAAAGCUU
+GUUGGUAGCUCCAGCAACGAUUGGGCUACUAGCUCCAUUUUCAACGUUUGCUGGC
diff -r 000000000000 -r 93a6f5eb2f9a test-data/input.fasta~
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.fasta~ Tue Jan 14 15:48:33 2014 -0500
@@ -0,0 +1,4 @@
+>AF165050.379
+UUGGGGGCGACAUUCCACCAUAGAUAAUUCCCCUGUGAGGAAUUACUGUUUUAACGCAGAAAGCGUUUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCUUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGAUGACCGGGUCCUUUCUUGGAUCAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAUCCUAAACCCCAAAGAAAAACCAAACGUAACACCAACCG
+>D45172.391
+GCCAGCCCCCUGAUGGGGGCGACACUCCACCAUAGAUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUCUUGGAUCAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAUCCAAAACCCCAAAGAAAAAUCAAACGUAACACCAACCG
diff -r 000000000000 -r 93a6f5eb2f9a tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue Jan 14 15:48:33 2014 -0500
@@ -0,0 +1,9 @@
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