Mercurial > repos > iuc > mothur_chimera_pintail
annotate chimera.pintail.xml @ 0:1e243f796db9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 05:17:01 -0400 |
parents | |
children | a037860aad0b |
rev | line source |
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0
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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1 <tool profile="16.07" id="mothur_chimera_pintail" name="Chimera.pintail" version="@WRAPPER_VERSION@.0"> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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2 <description>Find putative chimeras using pintail</description> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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3 <macros> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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4 <import>macros.xml</import> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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5 </macros> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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changeset
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6 <expand macro="requirements"/> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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7 <expand macro="stdio"/> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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changeset
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8 <expand macro="version_command"/> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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9 <command><![CDATA[ |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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10 @SHELL_OPTIONS@ |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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11 |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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12 ## create symlinks to input datasets |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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13 ln -s "$fasta" fasta.dat && |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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14 ln -s "$alignment.template" alignment.template.dat && |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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changeset
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15 ln -s "$conservation" conservation.dat && |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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changeset
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16 ln -s "$quantile" quantile.dat && |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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17 #if $mask.source2 == "history": |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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18 ln -s "$mask.input" mask.input.dat && |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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19 #end if |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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20 |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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changeset
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21 echo 'chimera.pintail( |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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22 fasta=fasta.dat, |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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23 reference=alignment.template.dat, |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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24 filter=$filter, |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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25 #if $mask.source2 == "default": |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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26 mask=default, |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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27 #elif $mask.source2 == "history": |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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28 mask=mask.input.dat, |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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29 #end if |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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30 #if $conservation: |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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31 conservation=conservation.dat, |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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32 #end if |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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changeset
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33 #if $quantile: |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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changeset
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34 quantile=quantile.dat, |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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changeset
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35 #end if |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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36 #if int($window) > 0: |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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changeset
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37 window=$window, |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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changeset
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38 #end if |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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changeset
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39 #if int($increment) > 0: |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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40 increment=$increment, |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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41 #end if |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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42 processors='\${GALAXY_SLOTS:-8}' |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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43 )' |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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44 | sed 's/ //g' ## mothur trips over whitespace |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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45 | mothur |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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46 | tee mothur.out.log |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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47 ]]></command> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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48 <inputs> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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49 <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
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50 <conditional name="alignment"> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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51 <param name="source" type="select" label="Select Reference Template from" help=""> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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52 <option value="hist">History</option> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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53 <option value="ref">Cached Reference</option> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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54 </param> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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55 <when value="ref"> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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56 <param name="template" type="select" label="reference - Select an alignment database" help=""> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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57 <options from_data_table="mothur_aligndb"/> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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58 </param> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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59 </when> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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60 <when value="hist"> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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61 <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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62 </when> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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63 </conditional> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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64 <param name="filter" type="boolean" falsevalue="false" truevalue="true" checked="false" label="filter - Apply a 50% soft vertical filter"/> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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65 <conditional name="mask"> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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66 <param name="source2" type="select" label="Mask option"> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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67 <option value="">None</option> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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68 <option value="default">default ecoli mask</option> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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69 <option value="history">From your history</option> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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70 </param> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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71 <when value="history"> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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72 <param name="input" type="data" format="mothur.filter" label="Mask for the template file" help=""/> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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73 </when> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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74 <when value=""/> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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75 <when value="default"/> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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76 </conditional> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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77 <param name="conservation" type="data" format="mothur.freq" optional="true" label="conservation - Template Conserved frequencies" help="a file containing the frequency information for your template file to increase speed. Mothur will generate this for you but it takes a long time."/> |
1e243f796db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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78 <param name="quantile" type="data" format="mothur.quan" optional="true" label="quantile - Template quantile information" help=" file containing the quantiles information for your template file to increase speed. Mothur can generate this for you but it takes a VERY long time. Note that when you use the filter, mask or mask and filter you need to select the appropriate quantile file. The filter parameter makes the quantile file generated specific to the query set you are analyzing."/> |
1e243f796db9
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79 <param name="window" type="integer" value="300" label="window - Length of sequence you want in each window analyzed (uses default if < 1)" help="Default is set to 300. Note, changing the window size will require new quantile files to be made."/> |
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80 <param name="increment" type="integer" value="25" label="increment - Increment for window slide on each iteration (uses default if < 1)" help="Default is 25. Note, changing the increment will require new quantile files to be made."/> |
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81 </inputs> |
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82 <outputs> |
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83 <expand macro="logfile-output"/> |
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84 <data name="out_file" format="txt" from_work_dir="fasta.*pintail.chimeras" label="${tool.name} on ${on_string}: pintail.chimeras"/> |
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85 <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*pintail.accnos" label="${tool.name} on ${on_string}: pintail.accnos"/> |
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86 <data name="out_freq" format="mothur.freq" from_work_dir="alignment.template.freq" label="${tool.name} on ${on_string}: pintail.freq"> |
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87 <filter>conservation == None</filter> |
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88 </data> |
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89 <data name="out_quantile" format="mothur.quan" from_work_dir="*.quan" label="${tool.name} on ${on_string}: pintail.quan"> |
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90 <filter>quantile == None</filter> |
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91 </data> |
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92 </outputs> |
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93 <tests> |
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94 <test> |
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95 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> |
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96 <param name="source" value="hist"/> |
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97 <param name="template" value="HMP_MOCK.v35.align"/> |
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98 <param name="quantile" value="HMP_MOCK.v35.pintail.quan"/> |
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99 <param name="window" value="200"/> |
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100 <output name="out_file" md5="644fe23ee459a76de7b225e530361865" ftype="txt"/> |
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101 <output name="out_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.pintail.accnos" ftype="mothur.accnos"/> |
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102 <expand macro="logfile-test"/> |
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103 </test> |
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104 <test> |
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105 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> |
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106 <param name="source" value="hist"/> |
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107 <param name="template" value="HMP_MOCK.v35.align"/> |
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108 <param name="source2" value="default"/> |
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109 <param name="window" value="200"/> |
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110 <output name="out_file" ftype="txt"> |
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111 <assert_contents> |
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112 <has_text text="Observed"/> |
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113 <has_text text="Expected"/> |
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114 </assert_contents> |
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115 </output> |
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116 <output name="out_quantile" md5="23a665c9bace6b73efaae1ecf6d88c59" ftype="mothur.quan"/> |
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117 <output name="out_freq" md5="0381c5adade485cc4341a0ef5674f4d8" ftype="mothur.freq"/> |
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118 <expand macro="logfile-test"/> |
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119 </test> |
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120 </tests> |
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121 <help> |
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122 <![CDATA[ |
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123 |
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124 @MOTHUR_OVERVIEW@ |
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125 |
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126 **Command Documentation** |
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127 |
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128 The chimera.pintail_ command identifies putative chimeras using the pintail approach. It looks at the variation between the expected differences and the observed differences in the query sequence over several windows. |
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129 |
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130 This method was written using the algorithms described in the paper_ "At Least 1 in 20 16S rRNA Sequence Records Currently Held in the Public Repositories is Estimated To Contain Substantial Anomalies" by Kevin E. Ashelford 1, Nadia A. Chuzhanova 3, John C. Fry 1, Antonia J. Jones 2 and Andrew J. Weightman 1. |
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131 |
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132 The Pintail algorithm is a technique for determining whether a 16S rDNA sequence is anomalous. It is based on the idea that the extent of local base differences between two aligned 16S rDNA sequences should be roughly the same along the length of the alignment (having allowed for the underlying pattern of hypervariable and conserved regions known to exist within the 16S rRNA gene). In other words, evolutionary distance between two reliable sequences should be constant along the length of the gene. |
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133 |
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134 In contrast, if an error-free sequence is compared with an anomalous sequence, evolutionary distance along the alignment is unlikely to be constant, especially if the anomaly in question is a chimera and formed from phylogenetically different parental sequences. |
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135 |
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136 The Pintail algorithm is designed to detect and quantify such local variations and in doing so generates the Deviation from Expectation (DE) statistic. The higher the DE value, the greater the likelihood that the query is anomalous. |
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137 |
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138 The algorithm works as follows |
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139 |
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140 The sequence to be checked (the query) is first globally aligned with a phylogenetically similar sequence known to be error-free (the subject). At regular intervals along the resulting alignment, the local evolutionary distance between query and subject is estimated by recording percentage base mismatches within a sampling window of fixed length. The resulting array of percentages (observed percentage differences) reflects variations in evolutionary distance between the query and subject along the length of the 16S rRNA gene. Subtracting observed percentage differences from an equivalent array of expected percentage differences (predicted values for error-free sequences), we obtain a set of deviations, the standard deviation of which (Deviation from Expectation, DE) summarises the variation between observed and expected datasets. The greater the DE value, the greater the disparity there is between observed and expected percentage differences, and the more likely it is that the query sequence is anomalous. |
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141 |
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142 |
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143 .. _paper: http://www.ncbi.nlm.nih.gov/pubmed/16332745 |
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144 .. _chimera.pintail: https://www.mothur.org/wiki/Chimera.pintail |
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145 |
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146 ]]> |
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147 </help> |
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148 <expand macro="citations"> |
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149 <citation type="doi">10.1128/AEM.71.12.7724-7736.2005</citation> |
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150 </expand> |
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151 </tool> |