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1 <tool id="splicesite" 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="splicesitescore/score5.pl" selected="true">5' splice site</option>
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8 <option value="splicesitescore/score3.pl">3' splice site</option>
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9 </param>
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10 </inputs>
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11 <outputs>
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12 <data format="tabular" name="out_file1" />
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13 </outputs>
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14 <help>
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15
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16 **What it does**
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17
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18 This tool computes splice site scores using a max entropy model. See more details here:
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19
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20 http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html
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21
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22 -----
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23
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24 **Example input for 5' splice site sequence**
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25
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26 3 exonic and 6 intronic nucleotides flanking the junction::
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27
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28 CTGGTGAGT
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29 AAGGTACAG
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30
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31 or fasta format::
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32
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33 >seq1
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34 CTGGTGAGT
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35 >seq2
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36 AAGGTACAG
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37
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38 Output::
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39
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40 CTGGTGAGT 10.10
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41 AAGGTACAG 8.04
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42
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43 or fasta format::
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44
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45 >seq1 CTGGTGAGT 10.10
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46 >seq2 AAGGTACAG 8.04
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47
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48
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49 -----
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50
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51 **Example input for 3' splice site sequence**
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52
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53 3 exonic and 20 intronic nucleotides flanking the junction::
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54
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55 CCTGCATCCTCTGTTCCCAGGTG
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56 TTTCTTCCCTCCGGGAACAGTGG
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57
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58 Output::
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59
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60 CCTGCATCCTCTGTTCCCAGGTG 10.47
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61 TTTCTTCCCTCCGGGAACAGTGG 6.22
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62
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63 </help>
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64 </tool>
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