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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="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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8
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10 <param name="genome" type="select" label="Select chromsome size file" >
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11 <options from_file="chrsize.loc">
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12 <column name="name" index="0"/>
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13 <column name="value" index="1"/>
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14 </options>
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15 </param>
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16
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0
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17 </inputs>
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18 <outputs>
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19 <data format="tabular" name="out_file1" />
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20 </outputs>
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21 <help>
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22
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23 **What it does**
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24
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25 This tool computes splice site scores using a max entropy model. See more details here:
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26
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27 http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html
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28
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29 -----
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30
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31 **Example input for 5' splice site sequence**
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32
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33 3 exonic and 6 intronic nucleotides flanking the junction::
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34
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35 CTGGTGAGT
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36 AAGGTACAG
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37
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38 or fasta format::
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39
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40 >seq1
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41 CTGGTGAGT
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42 >seq2
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43 AAGGTACAG
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44
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45 Output::
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46
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47 CTGGTGAGT 10.10
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48 AAGGTACAG 8.04
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49
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50 or fasta format::
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51
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52 >seq1 CTGGTGAGT 10.10
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53 >seq2 AAGGTACAG 8.04
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54
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55
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56 -----
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57
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58 **Example input for 3' splice site sequence**
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59
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60 3 exonic and 20 intronic nucleotides flanking the junction::
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61
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62 CCTGCATCCTCTGTTCCCAGGTG
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63 TTTCTTCCCTCCGGGAACAGTGG
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64
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65 Output::
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66
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67 CCTGCATCCTCTGTTCCCAGGTG 10.47
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68 TTTCTTCCCTCCGGGAACAGTGG 6.22
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69
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70 </help>
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71 </tool>
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