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Protocol search - Revision history
2024-03-28T14:07:29Z
Revision history for this page on the wiki
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https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Protocol_search&diff=17668&oldid=prev
Angermue at 15:07, 6 May 2012
2012-05-06T15:07:58Z
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 15:07, 6 May 2012</td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Calling blastpgp ==</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Calling blastpgp ==</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">[[File:</del>run_blastpgp.sh<del class="diffchange diffchange-inline">]]</del> is the script we used for performing several iterations blastpgp with <tt>P04062.seq</tt> as query sequence. It takes the number of iterations, the inclusion threshold, and the databases as input arguments and creates a BLAST output files and also a BLAST checkout file which refers to the PSSM used in the last search iteration:</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"><tt></ins>run_blastpgp.sh<ins class="diffchange diffchange-inline"></tt></ins> is the script we used for performing several iterations blastpgp with <tt>P04062.seq</tt> as query sequence. It takes the number of iterations, the inclusion threshold, and the databases as input arguments and creates a BLAST output files and also a BLAST checkout file which refers to the PSSM used in the last search iteration:</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The resulting checkpoint file was than used to jumpstart blastpgp via <del class="diffchange diffchange-inline">[[File:</del>run_blastpgp_chk.sh<del class="diffchange diffchange-inline">]]</del>:</div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The resulting checkpoint file was than used to jumpstart blastpgp via <ins class="diffchange diffchange-inline"><tt></ins>run_blastpgp_chk.sh<ins class="diffchange diffchange-inline"></tt></ins>:</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><pre></div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><pre></div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#!/bin/bash</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td>
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<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Calling HHblits ==</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Calling HHblits ==</div></td>
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<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">[[File:</del>run_hhblits.sh<del class="diffchange diffchange-inline">]]</del> is the caller script for HHblits which takes the number of iterations and the inclusion value as arguments:</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"><tt></ins>run_hhblits.sh<ins class="diffchange diffchange-inline"></tt></ins> is the caller script for HHblits which takes the number of iterations and the inclusion value as arguments:</div></td>
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<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><pre></div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><pre></div></td>
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<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#!/bin/bash</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#!/bin/bash</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>We made use of following scripts for carrying out the analysis:</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>We made use of following scripts for carrying out the analysis:</div></td>
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<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>{|class="wikitable"</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>{|class="wikitable"</div></td>
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<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>|<del class="diffchange diffchange-inline">[[File:</del>hits_blastpgp.pl<del class="diffchange diffchange-inline">]]</del> || Lists the e-evalue and sequence identity for all hits in a blastpgp output file.</div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>|<ins class="diffchange diffchange-inline"><tt></ins>hits_blastpgp.pl<ins class="diffchange diffchange-inline"></tt></ins> || Lists the e-evalue and sequence identity for all hits in a blastpgp output file.</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
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<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>|<del class="diffchange diffchange-inline">[[File:</del>hits_hhblits.pl<del class="diffchange diffchange-inline">]]</del> || Lists the e-evalue and sequence identity for all hits in a hhblits output file.</div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>|<ins class="diffchange diffchange-inline"><tt></ins>hits_hhblits.pl<ins class="diffchange diffchange-inline"></tt></ins> || Lists the e-evalue and sequence identity for all hits in a hhblits output file.</div></td>
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<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
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<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>|<del class="diffchange diffchange-inline">[[File:</del>hits_hhblits.pl<del class="diffchange diffchange-inline">]]</del> || Lists the e-evalue and sequence identity for all hits in a hhblits output file.</div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>|<ins class="diffchange diffchange-inline"><tt></ins>hits_hhblits.pl<ins class="diffchange diffchange-inline"></tt></ins> || Lists the e-evalue and sequence identity for all hits in a hhblits output file.</div></td>
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<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
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<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>|<del class="diffchange diffchange-inline">[[File:</del>getids.sh<del class="diffchange diffchange-inline">]]</del> || Extracts the sequence identifiers of a hit list.</div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>|<ins class="diffchange diffchange-inline"><tt></ins>getids.sh<ins class="diffchange diffchange-inline"></tt></ins> || Extracts the sequence identifiers of a hit list.</div></td>
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<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
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<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>|<del class="diffchange diffchange-inline">[[File:</del>filter_evalue.sh<del class="diffchange diffchange-inline">]]</del> || Filters a hit list by evalue.</div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>|<ins class="diffchange diffchange-inline"><tt></ins>filter_evalue.sh<ins class="diffchange diffchange-inline"></tt></ins> || Filters a hit list by evalue.</div></td>
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<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
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<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>|<del class="diffchange diffchange-inline">[[File:</del>filter_id.sh<del class="diffchange diffchange-inline">]]</del> || Filters a hit list by sequence identity.</div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>|<ins class="diffchange diffchange-inline"><tt></ins>filter_id.sh<ins class="diffchange diffchange-inline"></tt></ins> || Filters a hit list by sequence identity.</div></td>
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<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
<td class="diff-marker"> </td>
<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
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<td class="diff-marker">−</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>|<del class="diffchange diffchange-inline">[[File:</del>uptr.sh<del class="diffchange diffchange-inline">]]</del> || Lists all >tr/>sp identifiers for a list of >UP20 identifiers.</div></td>
<td class="diff-marker">+</td>
<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>|<ins class="diffchange diffchange-inline"><tt></ins>uptr.sh<ins class="diffchange diffchange-inline"></tt></ins> || Lists all >tr/>sp identifiers for a list of >UP20 identifiers.</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>|}</div></td>
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Angermue
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Protocol_search&diff=17663&oldid=prev
Angermue at 15:03, 6 May 2012
2012-05-06T15:03:01Z
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 15:03, 6 May 2012</td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Calling blastpgp ==</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>[[File:run_blastpgp.sh]] is the script we used for performing several iterations blastpgp with <tt>P04062.seq</tt> as query sequence. It creates a BLAST output files and also a BLAST checkout file which refers to the PSSM used in the last search iteration:</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>[[File:run_blastpgp.sh]] is the script we used for performing several iterations blastpgp with <tt>P04062.seq</tt> as query sequence. It<ins class="diffchange diffchange-inline"> takes the number of iterations, the inclusion threshold, and the databases as input arguments and</ins> creates a BLAST output files and also a BLAST checkout file which refers to the PSSM used in the last search iteration:</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>;HHblits</div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:<pre>run_hhblits.sh 2 1e-3</pre></div></td>
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<td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>:<pre>run_hhblits.sh 2 1e-3</pre></div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>We made use of following scripts for carrying out the analysis:</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>{|class="wikitable"</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>|[[File:hits_blastpgp.pl]] || Lists the e-evalue and sequence identity for all hits in a blastpgp output file.</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>|[[File:hits_hhblits.pl]] || Lists the e-evalue and sequence identity for all hits in a hhblits output file.</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>|[[File:hits_hhblits.pl]] || Lists the e-evalue and sequence identity for all hits in a hhblits output file.</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>|[[File:getids.sh]] || Extracts the sequence identifiers of a hit list.</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>|[[File:filter_evalue.sh]] || Filters a hit list by evalue.</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>|[[File:filter_id.sh]] || Filters a hit list by sequence identity.</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>|-</div></td>
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<td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>|[[File:uptr.sh]] || Lists all >tr/>sp identifiers for a list of >UP20 identifiers.</div></td>
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Angermue
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Protocol_search&diff=17657&oldid=prev
Angermue: Created page with "== Sources == The data and scripts we used can be found in <tt>/mnt/home/student/angermue/mp/tasks/task02/search</tt> == Calling blastpgp == File:run_blastpgp.sh is the scri…"
2012-05-06T14:51:46Z
<p>Created page with "== Sources == The data and scripts we used can be found in <tt>/mnt/home/student/angermue/mp/tasks/task02/search</tt> == Calling blastpgp == <a href="/wiki/index.php?title=File:Run_blastpgp.sh&action=edit&redlink=1" class="new" title="File:Run blastpgp.sh (page does not exist)">File:run_blastpgp.sh</a> is the scri…"</p>
<p><b>New page</b></p><div>== Sources ==<br />
The data and scripts we used can be found in <tt>/mnt/home/student/angermue/mp/tasks/task02/search</tt><br />
<br />
== Calling blastpgp ==<br />
[[File:run_blastpgp.sh]] is the script we used for performing several iterations blastpgp with <tt>P04062.seq</tt> as query sequence. It creates a BLAST output files and also a BLAST checkout file which refers to the PSSM used in the last search iteration:<br />
<br />
<pre><br />
#!/bin/bash<br />
<br />
SEQ=/mnt/home/student/angermue/mp/data/P04062.seq<br />
DIR=/mnt/home/student/angermue/mp/tasks/task02/search/blastpgp<br />
NAME=`basename $SEQ`<br />
NAME=${NAME%.*}<br />
j=${1:-1}<br />
h=${2:-2e-3}<br />
DB=${3:-/mnt/project/pracstrucfunc12/data/big/big_80}<br />
DIRBASENAME=$(printf '%s/blastpgp_i%s_d%s_j%d_h%g' $DIR $NAME `basename $DB` $j $h)<br />
<br />
/usr/bin/time -o $DIRBASENAME.time blastpgp \<br />
-i $SEQ -d $DB -a 2 -e 10 -v 10000 -b 10000 -j $j -h $h \<br />
-o $DIRBASENAME.bla -C $DIRBASENAME.chk > $DIRBASENAME.out<br />
</pre><br />
<br />
The resulting checkpoint file was than used to jumpstart blastpgp via [[File:run_blastpgp_chk.sh]]:<br />
<pre><br />
#!/bin/bash<br />
<br />
CHK=$1<br />
SEQ=/mnt/home/student/angermue/mp/data/P04062.seq<br />
DB=/mnt/project/pracstrucfunc12/data/big/big<br />
DIRBASENAME=$(printf '%s_d%s' $CHK `basename $DB`)<br />
<br />
/usr/bin/time -o $DIRBASENAME.time blastpgp \<br />
-i $SEQ -R $CHK -d $DB -a 2 -e 10 -v 10000 -b 10000 -j 1 \ <br />
-o $DIRBASENAME.bla > $DIRBASENAME.out<br />
</pre><br />
<br />
Altogether, following commands were executed to obtain the relevant BLAST/PSI-BLAST results:<br />
;BLAST<br />
: <pre> run_blastpgp.sh 1 2e-3 /mnt/project/pracstrucfunc12/data/big/big</pre><br />
;PSI-BLAST_j2_h2e-3<br />
: <pre> run_blastpgp.sh 2 2e-3 /mnt/project/pracstrucfunc12/data/big/big_80</pre><br />
: <pre> run_blastpgp_chk.sh /mnt/home/student/angermue/mp/tasks/task02/search/blastpgp/blastpgp_iP04062_dbig_80_j2_h0.002.chk</pre><br />
;PSI-BLAST_j2_h1e-10<br />
: <pre> run_blastpgp.sh 2 1e-10 /mnt/project/pracstrucfunc12/data/big/big_80</pre><br />
: <pre> run_blastpgp_chk.sh /mnt/home/student/angermue/mp/tasks/task02/search/blastpgp/blastpgp_iP04062_dbig_80_j2_h1e-10.chk</pre><br />
;PSI-BLAST_j10_h2e-3<br />
: <pre> run_blastpgp.sh 10 2e-3 /mnt/project/pracstrucfunc12/data/big/big_80</pre><br />
: <pre> run_blastpgp_chk.sh /mnt/home/student/angermue/mp/tasks/task02/search/blastpgp/blastpgp_iP04062_dbig_80_j10_h0.002.chk</pre><br />
;PSI-BLAST_j2_h1e-10<br />
: <pre> run_blastpgp.sh 10 1e-10 /mnt/project/pracstrucfunc12/data/big/big_80</pre><br />
: <pre> run_blastpgp_chk.sh /mnt/home/student/angermue/mp/tasks/task02/search/blastpgp/blastpgp_iP04062_dbig_80_j10_h1e-10.chk</pre><br />
<br />
== Calling HHblits ==<br />
[[File:run_hhblits.sh]] is the caller script for HHblits which takes the number of iterations and the inclusion value as arguments:<br />
<pre><br />
#!/bin/bash<br />
<br />
SEQ=/mnt/home/student/angermue/mp/data/P04062.seq<br />
DIR=/mnt/home/student/angermue/mp/tasks/task02/search/hhblits<br />
NAME=`basename $SEQ`<br />
NAME=${NAME%.*}<br />
DB=/mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current<br />
n=${1:-2}<br />
e=${1:-1e-3}<br />
DIRBASENAME=$(printf '%s/hhblits_i%s_d%s_n%d_e%g' $DIR $NAME `basename $DB` $n $e)<br />
<br />
/usr/bin/time -o $DIRBASENAME.time hhblits \<br />
-i $SEQ -d $DB -cpu 2 -E 10 -B 10000 -Z 10000 -n $n -e $e \<br />
-o $DIRBASENAME.hhr -oa3m $DIRBASENAME.a3m > $DIRBASENAME.out<br />
</pre><br />
The relevant HHblits results were obtained as follows:<br />
;HHblits<br />
:<pre>run_hhblits.sh 2 1e-3</pre></div>
Angermue