# HG changeset patch
# User yhoogstrate
# Date 1459412181 14400
# Node ID 22d7b6019372af3c8ca97d1b6b11b1c07ead2e8e
# Parent  27f670a42ba27ac2acd775cc24aa433c82baf096
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9

diff -r 27f670a42ba2 -r 22d7b6019372 README.rst
--- a/README.rst	Thu Dec 03 03:22:08 2015 -0500
+++ b/README.rst	Thu Mar 31 04:16:21 2016 -0400
@@ -5,6 +5,11 @@
 
 Segmentation-fold: An algorithm for predicting RNA 2D structures including K-turns
 
+Installation
+------------
+
+Requires a C++11 compliant compiler!
+
 Development
 -----------
 
diff -r 27f670a42ba2 -r 22d7b6019372 energy-estimation-utility.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/energy-estimation-utility.xml	Thu Mar 31 04:16:21 2016 -0400
@@ -0,0 +1,111 @@
+<tool id="energy_estimation_utility" name="energy-estimation-utility" version="1.6.3-0">
+    <description>Estimate the maximal energy a segment needs to assign to become part of the optimal structure using segmentation-fold</description>
+    
+    <requirements>
+        <requirement type="package" version="1.6.3">segmentation-fold</requirement>
+        <requirement type="package" version="2.7.10">python</requirement>
+    </requirements>
+    
+    <stdio></stdio>
+    
+    <version_command>segmentation-fold --version | head -n 2 | tail -n 1 | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//'</version_command>
+    
+    <command><![CDATA[
+        energy-estimation-utility
+            #if $parameters.use_custom_xml == "true"
+                -x "${parameters.input_xml}"
+            #else
+                -x "\$SEGMENTATION_FOLD_DEFAULT_XML"
+            #end if
+            
+            -r ${randomization.shuffle_n_times}
+        > "${output_list}"
+    ]]></command>
+    
+    <inputs>
+        <conditional name="parameters">
+            <param name="use_custom_xml"
+                type="boolean"
+                truevalue="true"
+                falsevalue="false"
+                selected="false"
+                label="Use segment definition from history" />
+
+            <when value="false" />
+            <when value="true">
+                <param name="input_xml"
+                    type="data"
+                    format="xml"
+                    multiple="false"
+                    argument="-x"
+                    label="Custom 'segments.xml'-syntaxed file" />
+            </when>
+        </conditional>
+        
+        <conditional name="randomization">
+            <param name="do_randomization"
+                type="boolean"
+                truevalue="true"
+                falsevalue="false"
+                selected="false"
+                label="Randomly shuffle the sequence(s) instead"
+                help="This can be helpful in determining a baseline of observing an energy parameter by chance" />
+
+            <when value="false">
+                <param name="shuffle_n_times"
+                       type="hidden"
+                       value="0"/>
+            </when>
+            <when value="true">
+                <param name="shuffle_n_times"
+                       type="integer"
+                       min="0"
+                       value="10" 
+                       argument="-r"
+                       label="Number of times the sequences have to be shuffled and energy parameters have to be estimated on" />
+            </when>
+        </conditional>
+    </inputs>
+    
+    <outputs>
+        <data format="text" name="output_list" label="${tool.name}" />
+    </outputs>
+    
+    <tests>
+        <test>
+            <param  name="use_custom_xml" value="true" />
+            <param  name="input_xml" value="segments_truncated.xml" ftype="xml" />
+            <param  name="do_randomization" value="false" />
+            <param  name="shuffle_n_times" value="0" />
+            
+            <output name="output_list" file="segments_truncated.out.txt" lines_diff="2" /><!-- Accept rounding errors by diff CPU's etc. -->
+        </test>
+        <test>
+            <param  name="use_custom_xml" value="true" />
+            <param  name="input_xml" value="segments_truncated.xml" ftype="xml" />
+            <param  name="do_randomization" value="false" />
+            <param  name="shuffle_n_times" value="1" />
+            
+            <output name="output_list" file="segments_truncated.2.out.txt" lines_diff="10" />
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+The tool uses the sequences from the xml file.
+    ]]></help>
+    
+    <citations>
+        <citation type="bibtex">
+           @mastersthesis{mastersthesis,
+              author       = {Youri Hoogstrate}, 
+              title        = {An algorithm for predicting RNA 2D structures including K-turns},
+              school       = {University of Technology Delft, Leiden University},
+              year         = 2012,
+              address      = {},
+              month        = 11,
+              note         = {Research assignment for Master Computer-science},
+              url          = { https://yh-kt-fold.googlecode.com/files/Report.pdf }
+            }
+        </citation>
+    </citations>
+</tool>
diff -r 27f670a42ba2 -r 22d7b6019372 scan-for-segments.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scan-for-segments.xml	Thu Mar 31 04:16:21 2016 -0400
@@ -0,0 +1,105 @@
+<tool id="scan_for_segments" name="scan-for-segments" version="1.6.3-0">
+    <description>Scan for the presence of segments in sequences using segmentation-fold</description>
+    
+    <requirements>
+        <requirement type="package" version="1.6.3">segmentation-fold</requirement>
+        <requirement type="package" version="2.7.10">python</requirement>
+    </requirements>
+    
+    <stdio></stdio>
+    
+    <version_command>segmentation-fold --version | head -n 2 | tail -n 1 | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//'</version_command>
+    
+    <command><![CDATA[
+        scan-for-segments
+            -T \${GALAXY_SLOTS:-4}
+            -x
+            #if str($parameters.use_custom_xml) == "true"
+                "${parameters.input_xml}"
+            #else
+                "\$SEGMENTATION_FOLD_DEFAULT_XML"
+            #end if
+            -p "in-depth"
+            "${input_fasta}"
+            
+            >   $output_list
+    ]]></command>
+
+    <inputs>
+        <param name="input_fasta"
+               type="data"
+               format="fasta"
+               argument="-f"
+               label="Fasta file with RNA-sequece" />
+
+        <conditional name="parameters">
+            <param name="use_custom_xml"
+                type="boolean"
+                truevalue="true"
+                falsevalue="false"
+                selected="false"
+                label="Use segment definition from history" />
+
+            <when value="false" />
+            <when value="true">
+                <param name="input_xml"
+                    type="data"
+                    format="xml"
+                    multiple="false"
+                    argument="-x"
+                    label="Custom 'segments.xml'-syntaxed file" />
+            </when>
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <data format="text" name="output_list" label="${tool.name} on ${str($input_fasta.hid) + ': ' + $input_fasta.name}" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_fasta" value="SNORD13-revised.fa" ftype="fasta" />
+            <param name="use_custom_xml" value="false" ftype="fasta" />
+            
+            <output name="output_list" file="SNORD13-revised.scan-for-segments.txt" />
+        </test>
+        <test>
+            <param name="input_fasta" value="SNORD48-revised.fa" ftype="fasta" />
+            <param name="use_custom_xml" value="false" ftype="fasta" />
+            
+            <output name="output_list" file="SNORD48-revised.scan-for-segments.txt" />
+        </test>
+        <test>
+            <param name="input_fasta" value="SNORD114-4-revised.fa" ftype="fasta" />
+            <param name="use_custom_xml" value="false" ftype="fasta" />
+            
+            <output name="output_list" file="SNORD114-4-revised.scan-for-segments.txt" />
+        </test>
+        <test>
+            <param name="input_fasta" value="SNORD118-revised.fa" ftype="fasta" />
+            <param name="use_custom_xml" value="false" ftype="fasta" />
+            
+            <output name="output_list" file="SNORD118-revised.scan-for-segments.txt" />
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+This is an utility of the segmentation-fold package that allows to scan for the presence of certain segments.
+If present, it will also scan for the Gibbs free energy necessairy the segment has to provide to contribute to the optimal structure.
+    ]]></help>
+    
+    <citations>
+        <citation type="bibtex">
+           @mastersthesis{mastersthesis,
+              author       = {Youri Hoogstrate}, 
+              title        = {An algorithm for predicting RNA 2D structures including K-turns},
+              school       = {University of Technology Delft, Leiden University},
+              year         = 2012,
+              address      = {},
+              month        = 11,
+              note         = {Research assignment for Master Computer-science},
+              url          = { https://yh-kt-fold.googlecode.com/files/Report.pdf }
+            }
+        </citation>
+    </citations>
+</tool>
diff -r 27f670a42ba2 -r 22d7b6019372 segmentation-fold.xml
--- a/segmentation-fold.xml	Thu Dec 03 03:22:08 2015 -0500
+++ b/segmentation-fold.xml	Thu Mar 31 04:16:21 2016 -0400
@@ -1,8 +1,8 @@
-<tool id="segmentation_fold" name="segmentation-fold" version="1.1.0_1">
+<tool id="segmentation_fold" name="segmentation-fold" version="1.6.3-0">
     <description>RNA-Folding including predefined segments including K-turns</description>
     
     <requirements>
-        <requirement type="package" version="1.1.0">segmentation-fold</requirement>
+        <requirement type="package" version="1.6.3">segmentation-fold</requirement>
     </requirements>
     
     <stdio></stdio>
@@ -61,7 +61,7 @@
     </inputs>
     
     <outputs>
-        <data format="dot-bracket" name="output_dbn" label="asdasdasd" />
+        <data format="dbn" name="output_dbn" label="segmentation-fold" />
         <!--<data format="dot-bracket" name="output_dbn" label="${tool.name} on ${str(input.input_fasta.hid) + ': ' + input.input_fasta.name if $input.method == 'fasta' else $input.input_sequence.upper() }" />-->
     </outputs>
     
@@ -181,16 +181,57 @@
     </tests>
     
     <help><![CDATA[
-Segmentation-fold is a bioinformatics application that predicts RNA
-2D-structure with an extended version of the Zuker algorithm. This
-modification contains a new "structure element" named a segment and is
-capable of folding a pre-defined substructures with multiple canonical
-or non-canonical pairings.
+**What it does**:
+
+Segmentation-fold is a application in the field of bioinformatics that
+predicts RNA 2D-structures. The model has an extension with respect to
+the classical Zuker algorithm, to allow new "structure elements" named
+segments and segmentloops. This makes it capable of folding a
+pre-defined substructure with multiple canonical or non-canonical base
+pairs, like K-turns and loop-E-motifs. Some of such sturcture elements
+are present in the corresponding energy table, although custom tables
+can be provided as well.
+
+
+**Running segmentation-fold**
+
+Segmentation-fold has to be provided with a sequence of which it has to
+predict the 2D structure. This can be done using a plain text sequence
+(allowed charset: ACTUG) or a FASTA file. A FASTA file has the following
+syntax:
+
+    >Sequence name and other details
+    
+    AGUGUAGCUGUGUCGAUCGUAAGUCAG
 
-This allows folding of more complex structures like K-turns, which are
-also part of the implemented free energy table. These thermodynamic
-parameters (free Gibbs energy) have been estimated using a in silico
-approach and therefore lack high resolution.
+As the database of free energy parameters will most likely be updated
+over time we have added the possiblity to include this XML file as
+additional parameter. The most up to date version of this file can be
+found at the following url:
+
+https://github.com/yhoogstrate/segmentation-fold/blob/master/share/segmentation-fold/segments.xml
+
+If you would like to compare the results with a prediction as if the
+segment and segmentloop extension were disabled, you can disable it with
+the given parameter.
+
+**Output**
+
+The output is in DotBracket format (dbn) and can be visualized with e.g.
+DrawRNAjs or VaRNA.
+
+DrawRNAjs can be installed in galaxy by following the instructions at
+the following link:
+
+https://github.com/bgruening/galaxytools/tree/master/visualisations/drawrnajs
+
+Details on the dbn-format can be found here:
+
+https://wiki.galaxyproject.org/Learn/Datatypes#Dbn
+
+**Authors**
+
+Youri Hoogstrate (yhoogstrate @ github)
     ]]></help>
     
     <citations>
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/SNORD114-4-revised.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SNORD114-4-revised.fa	Thu Mar 31 04:16:21 2016 -0400
@@ -0,0 +1,2 @@
+>SNORD114-4 revised
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/SNORD114-4-revised.scan-for-segments.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SNORD114-4-revised.scan-for-segments.txt	Thu Mar 31 04:16:21 2016 -0400
@@ -0,0 +1,74 @@
+>SNORD114-4 x Kt-42.dra
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-42.eco
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Loop-E-Motif.bac
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.UAU
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.UGU
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.CAU
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-42.tth
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-G2nA-SAM-riboswitch (T. tengcongensi)
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-7 G2nA SAM riboswitch (H. marismortui)
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-15.hma
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+.(((((((((.......)))))).((.((((..((..((((((..........)))))).))..))))..)))))	.((((((....(((.((.....((((......))))((....))...)...))))...(((....))).))))))	-6.4197063446
+>SNORD114-4 x Kt-U4b.hsa
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.GGU
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-7 (E. coli)
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-7 (D. radiodurans)
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-58.hma
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-46.tth
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-SAM-ribo.tte
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-23.eco
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-38.hma
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-46.dra
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.CGU
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-T-box.bsu
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-23.tth
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-46.eco
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-c-di-GMP-II.cac
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-11 (T. thermophilus)
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.AAU
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-L30e.sce
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-7 (T. thermophilus)
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-42.hma
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-U4a.hsa
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-G2nA-SAMribo.bsu
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.GAU
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-11.eco
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-46.hma
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.AGU
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+.(((((((((.......)))))).((.((((..((..((((((..........)))))).))..))))..)))))	.((((((...(((((.......((((......)))).((((((..........)))))).....)))))))))))	1.99971199036
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/SNORD118-revised.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SNORD118-revised.fa	Thu Mar 31 04:16:21 2016 -0400
@@ -0,0 +1,2 @@
+>SNORD118 revised
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/SNORD118-revised.scan-for-segments.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SNORD118-revised.scan-for-segments.txt	Thu Mar 31 04:16:21 2016 -0400
@@ -0,0 +1,75 @@
+>SNORD118 x Kt-42.dra
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-42.eco
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Loop-E-Motif.bac
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.UAU
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.UGU
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.CAU
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+.(((.((.(.(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).)))).)))))	.(((...((((((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).))))))))).	3.380651474
+>SNORD118 x Kt-42.tth
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-G2nA-SAM-riboswitch (T. tengcongensi)
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-7 G2nA SAM riboswitch (H. marismortui)
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-15.hma
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-U4b.hsa
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.GGU
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-7 (E. coli)
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-7 (D. radiodurans)
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-58.hma
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-46.tth
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-SAM-ribo.tte
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-23.eco
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-38.hma
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-46.dra
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.CGU
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+.(((.((.(.(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).)))).)))))	(((((...((((((............))...))))...))......(((((((((...........))))))))).....)))......	-15.021024704
+>SNORD118 x Kt-T-box.bsu
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-23.tth
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-46.eco
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-c-di-GMP-II.cac
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-11 (T. thermophilus)
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.AAU
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-L30e.sce
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-7 (T. thermophilus)
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-42.hma
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-U4a.hsa
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-G2nA-SAMribo.bsu
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.GAU
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+.(((.((.(.(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).)))).)))))	(((.(((...(((((......))))))((((.....))))...)).(((((((((...........))))))))).....)))......	-8.30012321472
+>SNORD118 x Kt-11.eco
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-46.hma
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.AGU
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/SNORD13-revised.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SNORD13-revised.fa	Thu Mar 31 04:16:21 2016 -0400
@@ -0,0 +1,2 @@
+>SNORD13 revised
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
\ No newline at end of file
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/SNORD13-revised.scan-for-segments.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SNORD13-revised.scan-for-segments.txt	Thu Mar 31 04:16:21 2016 -0400
@@ -0,0 +1,74 @@
+>SNORD13 x Kt-42.dra
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-42.eco
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Loop-E-Motif.bac
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.UAU
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.UGU
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.CAU
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-42.tth
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-G2nA-SAM-riboswitch (T. tengcongensi)
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-7 G2nA SAM riboswitch (H. marismortui)
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-15.hma
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-U4b.hsa
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.GGU
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-7 (E. coli)
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-7 (D. radiodurans)
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-58.hma
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-46.tth
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-SAM-ribo.tte
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-23.eco
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-38.hma
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-46.dra
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.CGU
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+(((((.(..((.(((....((((((((((((....)))))))(((((((..(.((((((...))).))).)..)))))))))))))))))..))))))	(((((.(.(...((((((.((((((((((((....)))))))(((((((..(.((((((...))).))).)..)))))))))))))))))))))))))	3.35026359558
+>SNORD13 x Kt-T-box.bsu
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-23.tth
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-46.eco
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-c-di-GMP-II.cac
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-11 (T. thermophilus)
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.AAU
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-L30e.sce
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-7 (T. thermophilus)
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-42.hma
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-U4a.hsa
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-G2nA-SAMribo.bsu
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.GAU
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+(((((.(..((.(((....((((((((((((....)))))))(((((((..(.((((((...))).))).)..)))))))))))))))))..))))))	(((((((.((((...((((((((((....))))))..)))))...)))))............((((.((((.((........)))))))))).)))))	-9.91994667053
+>SNORD13 x Kt-11.eco
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-46.hma
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.AGU
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/SNORD48-revised.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SNORD48-revised.fa	Thu Mar 31 04:16:21 2016 -0400
@@ -0,0 +1,2 @@
+>SNORD48 revised (2 extra bases on 5' end)
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
\ No newline at end of file
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/SNORD48-revised.scan-for-segments.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SNORD48-revised.scan-for-segments.txt	Thu Mar 31 04:16:21 2016 -0400
@@ -0,0 +1,74 @@
+>SNORD48 x Kt-42.dra
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-42.eco
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Loop-E-Motif.bac
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.UAU
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.UGU
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.CAU
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-42.tth
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-G2nA-SAM-riboswitch (T. tengcongensi)
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-7 G2nA SAM riboswitch (H. marismortui)
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-15.hma
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-U4b.hsa
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.GGU
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-7 (E. coli)
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-7 (D. radiodurans)
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-58.hma
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-46.tth
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-SAM-ribo.tte
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-23.eco
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-38.hma
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-46.dra
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.CGU
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-T-box.bsu
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-23.tth
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-46.eco
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-c-di-GMP-II.cac
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-11 (T. thermophilus)
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.AAU
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-L30e.sce
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-7 (T. thermophilus)
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-42.hma
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-U4a.hsa
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-G2nA-SAMribo.bsu
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.GAU
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+((((((.((.((((((((((.....)))).).).)))).((((...))))...)).))))))....	(((((...(((((((...))).....))))).....(((((............)))))))))....	-10.9206504822
+>SNORD48 x Kt-11.eco
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-46.hma
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.AGU
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+((((((.((.((((((((((.....)))).).).)))).((((...))))...)).))))))....	((...(((((..((..((((.....)))).))((((.((((((...))))..)).)))))))))))	-1.84962844849
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/segments_truncated.2.out.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/segments_truncated.2.out.txt	Thu Mar 31 04:16:21 2016 -0400
@@ -0,0 +1,5 @@
+>C/D-box snoRNA (shuffle iteration 1)
+agaggCGUGAUcccaacgUGAuggc
+....((((.......))))......	....(...((((.....)))))...	-9.3900680542
+>Artificial double C/D K-turn construct (shuffle iteration 1)
+uguucugucacggcacauaccuccggUGUGAUggUGAauaguaUGAgaaguaucgugugucagaggcccuaaUGUGAUgccuuaa
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/segments_truncated.out.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/segments_truncated.out.txt	Thu Mar 31 04:16:21 2016 -0400
@@ -0,0 +1,6 @@
+>C/D-box snoRNA
+GCUCUGACCGAAAGGCGUGAUGAGC
+((((....((.....))....))))	(((((((((....))...)))))))	2.50072479248
+>Artificial double C/D K-turn construct
+GGGAGUCUUGUGAUGAGAAGUACUGGAUCUGAAGUAGCCCUUUUUGGGCUACUUGUGAUGAAACACUCAUGGUCUGAAGACUCCC
+((((((((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).)))))))))	((((((((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..)))))))))))))	-1.25102996826
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/segments_truncated.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/segments_truncated.xml	Thu Mar 31 04:16:21 2016 -0400
@@ -0,0 +1,85 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<root>
+	<segments>
+		<segment>
+			<id>Kt-CD-box.UGU</id><!-- Common -->
+			<sequence_5prime>UGUGAU</sequence_5prime>
+			<bonds          >   :::</bonds>
+			<sequence_3prime>   AGU</sequence_3prime>
+			<energy>-11.1072</energy>
+			<directions>
+				<five_prime>true</five_prime>
+				<three_prime>true</three_prime>
+			</directions>
+		</segment>
+		
+		<segment>
+			<id>Kt-CD-box.CGU</id><!-- Common -->
+			<sequence_5prime>CGUGAU</sequence_5prime>
+			<bonds          >   :::</bonds>
+			<sequence_3prime>   AGU</sequence_3prime>
+			<energy>-11.1072</energy>
+			<directions>
+				<five_prime>true</five_prime>
+				<three_prime>true</three_prime>
+			</directions>
+		</segment>
+	</segments>
+	
+	
+	<segmentloops />
+	
+	
+	<!-- RNA-Molecules -->
+	<rnas>
+		<rna>
+			<title>C/D-box snoRNA</title>
+			<organism>A. fulgidus</organism>
+			<sequence>GCUCUGACCGAAAGGCGUGAUGAGC</sequence>
+			
+			<structures>
+				<structure>
+					<associated_segments>
+						<link>Kt-CD-box.CGU</link>
+					</associated_segments>
+					<dot_bracket type="full"   >(((((((((....))...)))))))</dot_bracket>
+				</structure>
+				
+				<structure>
+					<associated_segments />
+					<dot_bracket />
+				</structure>
+			</structures>
+			
+			<references>
+				<pdb>1RLG</pdb>
+				<url>http://www.sciencedirect.com/science/article/pii/S0969212604001169</url>
+			</references>
+		</rna>
+		
+		<rna>
+			<title>Artificial double C/D K-turn construct</title>
+			<sequence>GGGAGUCUUGUGAUGAGAAGUACUGGAUCUGAAGUAGCCCUUUUUGGGCUACUUGUGAUGAAACACUCAUGGUCUGAAGACUCCC</sequence>
+			
+			<structures>
+				<structure>
+					<associated_segments>
+						<link>Kt-CD-box.UGU</link>
+					</associated_segments>
+					<dot_bracket type="full"   >((((((((...((((?????????????((((((((((((.....))))))))...))))?????????????))))))))))))</dot_bracket>
+				</structure>
+				
+				<structure>
+					<associated_segments />
+					<dot_bracket />
+				</structure>
+			</structures>
+			
+			<references>
+				<pdb>3ICX</pdb>
+				<pdb>3ID6</pdb>
+				<doi>http://dx.doi.org/10.1038/nature09688</doi>
+			</references>
+		</rna>
+	</rnas>
+</root>
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_01.dbn
--- a/test-data/test_01.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_01.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 34bp, dE: -32.2572 kcal/mole
+>Sequence length: 34bp, dE: -28.56 kcal/mole, segments: 1
 CCAUGGGGAGCCGCACGGAGGCGAAGAACCAUGG
 ((((((((((((.......)))...)))))))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_02.dbn
--- a/test-data/test_02.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_02.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 34bp, dE: -34.4572 kcal/mole
+>Sequence length: 34bp, dE: -30.16 kcal/mole, segments: 1
 CCAGGGGGAGCCGGUAGCGGGCGUGGAUCCCUGG
 ((((((((((((.......)))...)))))))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_03.dbn
--- a/test-data/test_03.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_03.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 35bp, dE: -31.2572 kcal/mole
+>Sequence length: 35bp, dE: -26.76 kcal/mole, segments: 1
 CGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCG
 ((((((((((((.......))))....))))))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_04.dbn
--- a/test-data/test_04.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_04.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 34bp, dE: -30.4872 kcal/mole
+>Sequence length: 34bp, dE: -23.19 kcal/mole, segments: 1
 CCCCGACGAGCUGGAGAUACCCUUUGACUCGGGG
 ((((((((((..((.....)))...)))))))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_05.dbn
--- a/test-data/test_05.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_05.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 47bp, dE: -42.5072 kcal/mole
+>Sequence length: 47bp, dE: -34.71 kcal/mole, segments: 1
 CCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGG
 ((((.(((((..((((((((.......)))))))))))...))))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_06.dbn
--- a/test-data/test_06.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_06.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 47bp, dE: -40.3572 kcal/mole
+>Sequence length: 47bp, dE: -32.56 kcal/mole, segments: 1
 GGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCC
 ((((.(((((..((((((((.......)))))))))))...))))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_07.dbn
--- a/test-data/test_07.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_07.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 31bp, dE: -26.5072 kcal/mole
+>Sequence length: 31bp, dE: -24.51 kcal/mole, segments: 1
 AACCGAAGCCCUCACGGGCAAUGUGGUGUCA
-..(((.(((((....))))...)))).....
+.((((.(((((....))))...)))))....
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_08.dbn
--- a/test-data/test_08.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_08.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 37bp, dE: -33.7572 kcal/mole
+>Sequence length: 37bp, dE: -29.26 kcal/mole, segments: 1
 UUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAG
 ((((((((((((((......)))...)))))))))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_09.dbn
--- a/test-data/test_09.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_09.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 37bp, dE: -30.8072 kcal/mole
+>Sequence length: 37bp, dE: -26.31 kcal/mole, segments: 1
 UUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAG
 ((((((((((((((......)))...)))))))))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_10.dbn
--- a/test-data/test_10.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_10.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 109bp, dE: -76.7072 kcal/mole
+>Sequence length: 109bp, dE: -66.21 kcal/mole, segments: 1
 CUCCGCCGAGGUAGUCUGUGAGGUAGAGCGACCGAUUGGUGUGUCCGCCUCCGAGAGGAGUCGGCACACCUGUCAAACUCCAAACUUACAGACGCCGUUUGACGCGGGG
-((((((((((((.(((((((((...(((.(((..(..((((((.(((.((((....)))).)))))))))))))...)))....))))))))))))....)))))))))
+((((((((((((.(((((((((...(((.....(((.((((((.(((.((((....)))).))))))))).)))...)))....))))))))))))....)))))))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_11.dbn
--- a/test-data/test_11.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_11.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 53bp, dE: -46.6072 kcal/mole
+>Sequence length: 53bp, dE: -42.71 kcal/mole, segments: 1
 GGUGGUCUCGAGCCCUAGACAGCCGGUUUUUUCCGGCCGAGGUUUGAGGCGCC
 ((((.(((((((((...((.((((((......)))))))))))))))))))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_12.dbn
--- a/test-data/test_12.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_12.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 53bp, dE: -50.2072 kcal/mole
+>Sequence length: 53bp, dE: -46.31 kcal/mole, segments: 1
 GGAUGUGGCGCCGCGAAGACAGCCAGUUUUUUCUGGUCGAGUGGCGCCGCGCC
 ((.(((((((((((...((.((((((......)))))))))))))))))))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_13.dbn
--- a/test-data/test_13.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_13.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 53bp, dE: -43.5072 kcal/mole
+>Sequence length: 53bp, dE: -39.61 kcal/mole, segments: 1
 GGAUGUGUCGUCGCAUAGACAGCCAGUUUUUUCUGGUCGAGUGACGAUGCGCC
 ((.(((((((((((...((.((((((......)))))))))))))))))))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_14.dbn
--- a/test-data/test_14.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_14.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 53bp, dE: -37.9072 kcal/mole
+>Sequence length: 53bp, dE: -34.01 kcal/mole, segments: 1
 CGAUGUGGGAAGGCCCAGACAGCCAGUUUUUUCUGGUCGAGUCGGCCUGCGCG
 ((.((..((..(((...((.((((((......)))))))))))..))..))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_15.dbn
--- a/test-data/test_15.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_15.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 49bp, dE: -37.8572 kcal/mole
+>Sequence length: 49bp, dE: -32.16 kcal/mole, segments: 1
 CUCUAAUUGGAUGGAAGUAGGGGUGAAAACUCCUAUGGACCGAUUAGUG
 (.((((((((...(((((((((((....))))))))))))))))))).)
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_16.dbn
--- a/test-data/test_16.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_16.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 50bp, dE: -43.4072 kcal/mole
+>Sequence length: 50bp, dE: -34.51 kcal/mole, segments: 1
 UUCCCGAUGCCGAUGAAGGCCGACCCGCGAGGCGGCUGGAGGUAAGGGAA
-(((((...(((...((((((((..((....)))))))))))))..)))))
+(((((..((((...((((((((.((.....)))))))))))))).)))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_17.dbn
--- a/test-data/test_17.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_17.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 49bp, dE: -37.3072 kcal/mole
+>Sequence length: 49bp, dE: -30.91 kcal/mole, segments: 1
 UUCAGUCCGCGGUGAAGCCAUACCGGAAGGAGUGGUGGAGCCGACUGAA
 (((((((.((...((((((((.((....)).)))))))))).)))))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_18.dbn
--- a/test-data/test_18.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_18.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 50bp, dE: -37.7072 kcal/mole
+>Sequence length: 50bp, dE: -30.61 kcal/mole, segments: 1
 UUCUGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAA
 (((((...(((...(((((((((((....))))))))))))))..)))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_19.dbn
--- a/test-data/test_19.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_19.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 30bp, dE: -28.4572 kcal/mole
+>Sequence length: 30bp, dE: -24.46 kcal/mole, segments: 1
 UCCGUGGAAGCCGUAAUGGCAGGAAGCGGA
-((((((((.(((.....)))..))))))))
+((((((((.((((...))))..))))))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_20.dbn
--- a/test-data/test_20.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_20.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 22bp, dE: -23.2072 kcal/mole
+>Sequence length: 22bp, dE: -19.11 kcal/mole, segments: 1
 GCCAAUGAGGUUUAUCCGAGGC
 (((...((((.....)))))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_21.dbn
--- a/test-data/test_21.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_21.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 34bp, dE: -27.7072 kcal/mole
+>Sequence length: 34bp, dE: -22.71 kcal/mole, segments: 1
 ACGCAUAUCAGUGAGGAUUCGUCCGAGAUUGUGU
 (((((.(((...(((((....)))))))))))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_22.dbn
--- a/test-data/test_22.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_22.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 25bp, dE: -24.4072 kcal/mole
+>Sequence length: 25bp, dE: -18.01 kcal/mole, segments: 1
 GCUCUGACCGAAAGGCGUGAUGAGC
 (((((((((....))...)))))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_23.dbn
--- a/test-data/test_23.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_23.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 85bp, dE: -70.4144 kcal/mole
+>Sequence length: 85bp, dE: -60.91 kcal/mole, segments: 2
 GGGAGUCUUGUGAUGAGAAGUACUGGAUCUGAAGUAGCCCUUUUUGGGCUACUUGUGAUGAAACACUCAUGGUCUGAAGACUCCC
-((((((((...(((((..(((......(((((((((((((.....))))))))...)))))...))).....)))))))))))))
+((((((((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..)))))))))))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_24.dbn
--- a/test-data/test_24.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_24.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 34bp, dE: -29.0072 kcal/mole
+>Sequence length: 34bp, dE: -25.41 kcal/mole, segments: 1
 GGACGCAGAGAUGGUCUUUUUGACCGGAGUGUCC
 ((((((...(((((((.....)))))))))))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_25.dbn
--- a/test-data/test_25.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_25.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 26bp, dE: -24.7072 kcal/mole
+>Sequence length: 26bp, dE: -20.41 kcal/mole, segments: 1
 GGUGGAGGGACUGGCCCGAUGAAACC
 (((((((((.....)))...))))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_26.dbn
--- a/test-data/test_26.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_26.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 55bp, dE: -42.1072 kcal/mole
+>Sequence length: 55bp, dE: -33.71 kcal/mole, segments: 1
 GGGAGUAAAGAUUGAGACAAGUAGGACUUCGGUCCGAAUACACUCAUGAACUCCC
-((((((...(((((((....(((((((....))))...))).)))))))))))))
+((((((...(((((((...(((...)))(((...))).....)))))))))))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_27.dbn
--- a/test-data/test_27.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_27.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 36bp, dE: -26.2072 kcal/mole
+>Sequence length: 36bp, dE: -22.71 kcal/mole, segments: 1
 AACAAUGAUGAAUGGGUUUUUUACUCAUUUUGAGUU
 (((...(((((((((((.....))))))))))))))
diff -r 27f670a42ba2 -r 22d7b6019372 test-data/test_28.dbn
--- a/test-data/test_28.dbn	Thu Dec 03 03:22:08 2015 -0500
+++ b/test-data/test_28.dbn	Thu Mar 31 04:16:21 2016 -0400
@@ -1,3 +1,3 @@
->Sequence length: 26bp, dE: -24.7072 kcal/mole
+>Sequence length: 26bp, dE: -20.41 kcal/mole, segments: 1
 GGUGAAGGGACUGGCCCGACGAAACC
 (((((((((.....)))...))))))
diff -r 27f670a42ba2 -r 22d7b6019372 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Dec 03 03:22:08 2015 -0500
+++ b/tool_dependencies.xml	Thu Mar 31 04:16:21 2016 -0400
@@ -1,6 +1,10 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="segmentation-fold" version="1.1.0">
-        <repository changeset_revision="2c69127ea0cd" name="package_segmentation_fold_1_1_0" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="segmentation-fold" version="1.6.3">
+        <repository changeset_revision="a6b5d3d4825c" name="package_segmentation_fold_1_6_3" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    
+    <package name="python" version="2.7.10">
+        <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>