Mercurial > repos > rnateam > graphclust_mlocarna
annotate locarna_best_subtree.xml @ 0:15bd4fb05e5c draft
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
author | rnateam |
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date | Fri, 16 Dec 2016 07:35:29 -0500 |
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children | c6c4a7adb099 |
rev | line source |
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15bd4fb05e5c
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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1 <tool id="locarna_best_subtree" name="locarna_best_subtree" version="0.1.0" > |
15bd4fb05e5c
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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2 <requirements> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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3 <requirement type="package" version="0.1">graphclust-wrappers</requirement> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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4 <requirement type="package" version='1.8.10'>locarna</requirement> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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5 <requirement type="package" version='2.1'>rnaz</requirement> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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6 <requirement type="package" version='0.07'>perl-math-round</requirement> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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7 </requirements> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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8 <stdio> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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9 <exit_code range="1:" /> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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10 </stdio> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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11 <command> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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12 <![CDATA[ |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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13 |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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14 'locARNAGraphClust.pl' '$center_fa_file' '$tree_file' '$tree_matrix' $p $max_diff_am $tau $max_diff '' '$data_map' $plfold_minlen |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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15 ]]> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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16 </command> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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17 <inputs> |
15bd4fb05e5c
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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18 <param type="data" name="center_fa_file" label="centers" format="fa, fasta" help="fasta format" /> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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19 <param type="data" name="tree_file" label="trees" format="text" help="text format" /> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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20 <param type="data" name="tree_matrix" label="tree_matrix" format="text" help="text format" /> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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21 <param type="data" name="data_map" label="data_map" format="txt" help="text format" /> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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22 <param name="p" type="float" value="0.001" size="5" label="minimal probability" help="-p"/> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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23 <param name="max_diff_am" type="integer" value="50" size="5" label=" maximal difference for sizes of matched arcs" help="--max-diff-am"/> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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24 <param name="tau" type="integer" value="50" size="5" label="Tau factor in percent" help="--tau"/> |
15bd4fb05e5c
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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25 <param name="max_diff" type="integer" value="100" size="5" label="maximal difference for alignment traces" help="--max-diff"/> |
15bd4fb05e5c
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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26 <param name="plfold_minlen" type="integer" value="210" size="5" label="Minimal length of a sequences for which RNAplfold is used" /> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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27 </inputs> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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28 <outputs> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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29 |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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30 <data name="model_tree_stk" format="stockholm" label="model.tree.stk" from_work_dir="MODEL/best_subtree.aln" /> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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31 </outputs> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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32 <tests> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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33 <test> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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34 <param name="tree_file" value="1.1.tree"/> |
15bd4fb05e5c
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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35 <param name="center_fa_file" value="1.1.center.fa"/> |
15bd4fb05e5c
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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36 <param name="data_map" value="data.map"/> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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37 <param name="tree_matrix" value="1.1.matrix.tree"/> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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38 <param name="p" value="0.001"/> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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39 <param name="max-diff-am" value="50"/> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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40 <param name="tau" value="50"/> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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41 <param name="max-diff-am" value="100"/> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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42 <output name="model_tree_stk" file="best_subtree.aln"/> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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43 </test> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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44 </tests> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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45 <help> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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46 <![CDATA[ |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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47 **What it does** |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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48 |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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49 MLocARNA computes a multiple sequence-structure alignment of RNA sequences. |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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50 It uses *treefile* - file with guide tree in NEWICK format. The given tree is used as guide tree for the progressive alignment. |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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51 This saves the calculation of pairwise all-vs-all similarities and construction of the guide tree. |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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52 |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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53 |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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54 |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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55 ]]> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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56 </help> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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57 <citations> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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58 <citation type="bibtex">@inproceedings{costa2010fast, |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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59 title={Fast neighborhood subgraph pairwise distance kernel}, |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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60 author={Costa, Fabrizio and De Grave, Kurt}, |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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61 booktitle={Proceedings of the 26th International Conference on Machine Learning}, |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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62 pages={255--262}, |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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63 year={2010}, |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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64 organization={Omnipress} |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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65 } |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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66 </citation> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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67 <citation type="bibtex">@Article{Will_Joshi_Hofacker-LocAR_Accur_bound-2012, |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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68 author = {Will, Sebastian and Joshi, Tejal and Hofacker, Ivo L. and |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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69 Stadler, Peter F. and Backofen, Rolf}, |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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70 title = {{LocARNA}-{P}: {Accurate} boundary prediction and improved |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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71 detection of structural {RNAs}}, |
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72 journal = {RNA}, |
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73 year = {2012}, |
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74 volume = {18}, |
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75 number = {5}, |
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76 pages = {900-14}, |
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77 user = {will}, |
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78 pmid = {22450757}, |
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79 doi = {10.1261/rna.029041.111}, |
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80 issn = {1469-9001}, |
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81 issn = {1355-8382}, |
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82 abstract = {Current genomic screens for noncoding RNAs (ncRNAs) predict |
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83 a large number of genomic regions containing potential |
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84 structural ncRNAs. The analysis of these data requires |
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85 highly accurate prediction of ncRNA boundaries and |
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86 discrimination of promising candidate ncRNAs from weak |
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87 predictions. Existing methods struggle with these goals |
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88 because they rely on sequence-based multiple sequence |
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89 alignments, which regularly misalign RNA structure and |
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90 therefore do not support identification of structural |
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91 similarities. To overcome this limitation, we compute |
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92 columnwise and global reliabilities of alignments based on |
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93 sequence and structure similarity; we refer to these |
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94 structure-based alignment reliabilities as STARs. The |
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95 columnwise STARs of alignments, or STAR profiles, provide a |
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96 versatile tool for the manual and automatic analysis of |
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97 ncRNAs. In particular, we improve the boundary prediction of |
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98 the widely used ncRNA gene finder RNAz by a factor of 3 from |
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99 a median deviation of 47 to 13 nt. Post-processing RNAz |
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100 predictions, LocARNA-P's STAR score allows much stronger |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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101 discrimination between true- and false-positive predictions |
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102 than RNAz's own evaluation. The improved accuracy, in this |
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103 scenario increased from AUC 0.71 to AUC 0.87, significantly |
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104 reduces the cost of successive analysis steps. The |
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105 ready-to-use software tool LocARNA-P produces |
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106 structure-based multiple RNA alignments with associated |
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107 columnwise STARs and predicts ncRNA boundaries. We provide |
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108 additional results, a web server for LocARNA/LocARNA-P, and |
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109 the software package, including documentation and a pipeline |
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110 for refining screens for structural ncRNA, at |
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111 http://www.bioinf.uni-freiburg.de/Supplements/LocARNA-P/.} |
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112 } |
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113 </citation> |
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114 <citation type="bibtex">@Article{Will:etal:_infer_non_codin_rna_famil:PLOS2007, |
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115 author = {Sebastian Will and Kristin Reiche and Ivo L. Hofacker and |
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116 Peter F. Stadler and Rolf Backofen}, |
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117 title = {Inferring Non-Coding {RNA} Families and Classes by Means of |
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118 Genome-Scale Structure-Based Clustering}, |
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119 journal = {PLoS Comput Biol}, |
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120 year = 2007, |
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121 volume = {3}, |
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122 number = {4}, |
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123 pages = {e65}, |
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124 issn = {1553-7358}, |
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125 issn = {1553-734X}, |
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126 pmid = {17432929}, |
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127 doi = {10.1371/journal.pcbi.0030065}, |
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128 user = {will}, |
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129 abstract = {The RFAM database defines families of ncRNAs by means of |
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130 sequence similarities that are sufficientto establish |
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131 homology. In some cases, such as microRNAs, box H/ACA |
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132 snoRNAs, functional commonalities define classes of RNAs |
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133 that are characterized by structural similarities, and |
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134 typically consist ofmultiple RNA families. Recent advances |
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135 in high-throughput transcriptomics and comparative genomics |
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136 have produced very large sets of putative non-coding RNAs |
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137 and regulatory RNA signals. For many ofthem, evidence for |
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138 stabilizing selection acting on their secondary structures |
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139 has been derived, and at least approximate models of their |
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140 structures have been computed. The overwhelming majority of |
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141 these hypo-thetical RNAs cannot be assigned to established |
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142 families or classes. We present here a structure-based |
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143 clustering approach that is capable of extracting putative |
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144 RNA classesfrom genome-wide surveys for structured RNAs. The |
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145 LocARNA tool implements a novel variant of theSankoff |
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146 algorithm that is sufficiently fast to deal with several |
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147 thousand candidate sequences. The method is also robust |
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148 against false positive predictions, i.e., a contamination of |
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149 the input data with unstructured ornon-conserved |
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150 sequences. We have successfully tested the LocARNA-based |
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151 clustering approach on the sequences of the |
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152 RFAM-seedalignments. Furthermore, we have applied it to a |
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153 previously published set of 3332 predicted structured |
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154 elements in the Ciona intestinalis genomes (Missal et al., |
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155 Bioinformatics 21(S2), i77-i78). In addition torecovering |
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156 e.g. tRNAs as a structure-based class, the method identifies |
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157 several RNA families, including microRNA and snoRNA |
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158 candidates, and suggests several novel classes of ncRNAs for |
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159 which to-date norepresentative has been experimentally |
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160 characterized.} |
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161 } |
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162 |
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163 </citation> |
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164 <citation type="bibtex">@Article{Smith:Heyne:Richter:Freib_RNA_Tools:NAR2010, |
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165 author = {Smith, Cameron and Heyne, Steffen and Richter, Andreas S. |
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166 and Will, Sebastian and Backofen, Rolf}, |
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167 title = {Freiburg {RNA} {Tools}: a web server integrating {IntaRNA}, |
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168 {ExpaRNA} and {LocARNA}}, |
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169 journal = NAR, |
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170 year = {2010}, |
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171 volume = {38 Suppl}, |
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172 number = {}, |
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173 pages = {W373-7}, |
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174 user = {arichter}, |
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175 pmid = {20444875}, |
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176 doi = {10.1093/nar/gkq316}, |
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177 issn = {0305-1048}, |
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178 issn = {1362-4962}, |
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179 abstract = {The Freiburg RNA tools web server integrates three tools |
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180 for the advanced analysis of RNA in a common web-based user |
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181 interface. The tools IntaRNA, ExpaRNA and LocARNA support |
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182 the prediction of RNA-RNA interaction, exact RNA matching |
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183 and alignment of RNA, respectively. The Freiburg RNA tools |
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184 web server and the software packages of the stand-alone |
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185 tools are freely accessible at |
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186 http://rna.informatik.uni-freiburg.de.} |
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187 } |
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188 </citation> |
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189 </citations> |
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190 </tool> |