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11
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1 <tool id="maxent" name="splice site score">
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2 <description>using max entropy model</description>
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3 <command interpreter="perl">$script $input > $out_file1 </command>
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4 <inputs>
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5 <param name="input" format="txt" type="data" label="Sequence file" help="fasta or raw sequence (one sequence per line)"/>
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6 <param name="script" type="select" label="Select model">
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7 <option value="maxent_score5.pl" selected="true">5' splice site</option>
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8 <option value="maxent_score3.pl">3' splice site</option>
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9 </param>
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10
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11 </inputs>
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12 <outputs>
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13 <data format="tabular" name="out_file1" />
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14 </outputs>
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15 <help>
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16
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17 **What it does**
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18
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19 This tool computes splice site scores using a max entropy model. See more details here:
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20
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21 http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html
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22
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23 -----
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24
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25 **Example input for 5' splice site sequence**
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26
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27 3 exonic and 6 intronic nucleotides flanking the junction::
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28
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29 CTGGTGAGT
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30 AAGGTACAG
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31
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32 or fasta format::
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33
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34 >seq1
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35 CTGGTGAGT
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36 >seq2
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37 AAGGTACAG
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38
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39 Output::
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40
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41 CTGGTGAGT 10.10
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42 AAGGTACAG 8.04
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43
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44 or fasta format::
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45
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46 >seq1 CTGGTGAGT 10.10
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47 >seq2 AAGGTACAG 8.04
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48
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49
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50 -----
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51
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52 **Example input for 3' splice site sequence**
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53
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54 3 exonic and 20 intronic nucleotides flanking the junction::
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55
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56 CCTGCATCCTCTGTTCCCAGGTG
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57 TTTCTTCCCTCCGGGAACAGTGG
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58
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59 Output::
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60
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61 CCTGCATCCTCTGTTCCCAGGTG 10.47
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62 TTTCTTCCCTCCGGGAACAGTGG 6.22
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63
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64 </help>
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65 </tool>
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