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1 <tool id="predictnls" name="PredictNLS" version="0.0.4">
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2 <description>Find nuclear localization signals (NLSs) in protein sequences</description>
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3 <command interpreter="python">
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4 predictnls.py $fasta_file $tabular_file
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5 </command>
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6 <inputs>
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7 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
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8 </inputs>
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9 <outputs>
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10 <data name="tabular_file" format="tabular" label="predictNLS results" />
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11 </outputs>
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12 <tests>
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13 <test>
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14 <param name="fasta_file" value="four_human_proteins.fasta"/>
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15 <output name="tabular_file" file="four_human_proteins.predictnls.tabular"/>
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16 </test>
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17 </tests>
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18 <requirements>
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19 <requirement type="binary">predictnls</requirement>
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20 </requirements>
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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 calls a Python re-implementation of the PredictNLS tool for prediction of
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26 nuclear localization signals (NLSs), which works by looking for matches to
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27 a known set of patterns (described using regular expressions).
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28
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29 The input is a FASTA file of protein sequences, and the output is tabular with
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30 these columns (multiple rows per protein):
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31
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32 ====== ==========================================================================
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33 Column Description
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34 ------ --------------------------------------------------------------------------
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35 1 Sequence identifier
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36 2 Start of NLS
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37 3 NLS sequence
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38 4 NLS pattern (regular expression)
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39 5 Number of reference proteins with this NLS
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40 6 Percentage of reference proteins with this NLS which are nuclear localized
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41 7 Comma separated list of reference proteins
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42 8 Comma separated list of reference proteins' localizations
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43 ====== ==========================================================================
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44
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45 If a sequence has no predicted NLS, then there is no line in the output file
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46 for it. This is a simplification of the text rich output from the command line
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47 tool, to give a tabular file suitable for use within Galaxy.
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48
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49 Information about potential DNA binding (shown in the original predictnls
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50 tool) is not given.
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51
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52 **Localizations**
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53
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54 The following abbreviations are used (derived from SWISS-PROT):
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55
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56 ==== =======================
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57 Abbr Localization
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58 ---- -----------------------
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59 cyt Cytoplasm
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60 pla Chloroplast
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61 ret Eendoplasmic reticululm
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62 ext Extracellular
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63 gol Golgi
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64 lys Lysosomal
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65 mit Mitochondria
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66 nuc Nuclear
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67 oxi Peroxisom
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68 vac Vacuolar
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69 rip Periplasmic
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70 ==== =======================
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71
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72 **References**
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73
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74 Murat Cokol, Rajesh Nair, and Burkhard Rost.
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75 Finding nuclear localization signals.
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76 EMBO reports 1(5), 411–415, 2000
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77 http://dx.doi.org/10.1093/embo-reports/kvd092
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78
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79 http://rostlab.org
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80
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81 </help>
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82 </tool>
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