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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#44546A;mso-fareast-language:EN-US">Hi Anand,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#44546A;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#44546A;mso-fareast-language:EN-US">if you run “shuffleseq –help” you will see the type of input and output sequences.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#44546A;mso-fareast-language:EN-US">Version: EMBOSS:6.5.7.0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#44546A;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#44546A;mso-fareast-language:EN-US"> Standard (Mandatory) qualifiers:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#44546A;mso-fareast-language:EN-US"> [-sequence] seqall Sequence(s) filename and optional format, or<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#44546A;mso-fareast-language:EN-US"> reference (input USA)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#44546A;mso-fareast-language:EN-US"> [-outseq] seqoutall [<sequence>.<format>] Sequence set(s)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#44546A;mso-fareast-language:EN-US"> filename and optional format (output USA)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#44546A;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#44546A;mso-fareast-language:EN-US">The “all” in seqall and seqoutall indicates that input and output can be sequence files with multiple sequences.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#44546A;mso-fareast-language:EN-US">This can be fasta format or any other sequence format supported by EMBOSS (genbank, embl etc.)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#44546A;mso-fareast-language:EN-US">The names of the sequences as they are in the original file, will be preserved in the output file.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#44546A;mso-fareast-language:EN-US">If I try to reproduce your example with the file downloaded from IPK:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#44546A;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#44546A;mso-fareast-language:EN-US">shuffleseq Athaliana_167_TAIR9.fa test1.fa<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#44546A;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#44546A;mso-fareast-language:EN-US">the output file contains the sequences as named in the input file:<br>
<br>
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#44546A;mso-fareast-language:EN-US">infoseq -only -name -desc test1.fa<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#44546A;mso-fareast-language:EN-US">Name Description<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#44546A;mso-fareast-language:EN-US">Chr1 CHROMOSOME dumped from ADB: Feb/3/09 16:9; last updated: 2007-12-20<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#44546A;mso-fareast-language:EN-US">Chr2 CHROMOSOME dumped from ADB: Feb/3/09 16:10; last updated: 2007-12-20<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#44546A;mso-fareast-language:EN-US">Chr3 CHROMOSOME dumped from ADB: Feb/3/09 16:10; last updated: 2007-12-20<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#44546A;mso-fareast-language:EN-US">Chr4 CHROMOSOME dumped from ADB: Feb/3/09 16:10; last updated: 2007-12-20<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#44546A;mso-fareast-language:EN-US">Chr5 CHROMOSOME dumped from ADB: Feb/3/09 16:10; last updated: 2007-12-20<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#44546A;mso-fareast-language:EN-US">ChrM CHROMOSOME dumped from ADB: Feb/3/09 16:10; last updated: 2005-06-03<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#44546A;mso-fareast-language:EN-US">ChrC CHROMOSOME dumped from ADB: Feb/3/09 16:10; last updated: 2005-06-03<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#44546A;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#44546A;mso-fareast-language:EN-US">Your input file contains in the name “shIDscleaned-up”. You may have done some modifications to the sequence names which confuse EMBOSS.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#44546A;mso-fareast-language:EN-US">You can test this by running the infoseq as above and check if you get for “Name” what you expect.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#44546A;mso-fareast-language:EN-US">Make sure you don’t have any “:” characters in the sequence names in your fasta file. This character has a special meaning in EMBOSS sequence names.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#44546A;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#44546A;mso-fareast-language:EN-US">Hope this helps.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#44546A;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#44546A;mso-fareast-language:EN-US">Sincerely,
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#44546A;mso-fareast-language:EN-US">David.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-family:"Calibri",sans-serif;color:#44546A;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="DE" style="font-size:11.0pt;font-family:"Calibri",sans-serif">Von:</span></b><span lang="DE" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> EMBOSS <emboss-bounces+david.bauer=bayer.com@mailman.open-bio.org>
<b>Im Auftrag von </b>Anandkumar Surendrarao<br>
<b>Gesendet:</b> 09 November 2018 04:20<br>
<b>An:</b> emboss@mailman.open-bio.org<br>
<b>Betreff:</b> [EMBOSS] shuffleseq for multifasta?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE"><o:p> </o:p></span></p>
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<p class="MsoNormal">Greetings!<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I am new to EMBOSS, and trying to use shufflseq to randomly shuffle entire genomes (one-by-one). My input genomic sequences are in multifasta format. And I wish to retain the same multifasta format for the output file as well, containing
the shuffled DNA sequences.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">From the information at <a href="http://emboss.sourceforge.net/apps/cvs/emboss/apps/shuffleseq.html" target="_blank">http://emboss.sourceforge.net/apps/cvs/emboss/apps/shuffleseq.html</a>, it appears to me that FASTA format for neither
input not output is supported. Am I mistaken?<o:p></o:p></p>
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<p class="MsoNormal">OR <o:p></o:p></p>
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<p class="MsoNormal">Is there a way to specify (multi)FASTA as both input and output formats?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">In one run that I completed with a genome assembly with 5 chromosmes - Chr1 ... Chr5, the syntax I used was:<o:p></o:p></p>
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<p class="MsoNormal">shuffleseq -sequence Athaliana_167_TAIR9.fa.shIDscleaned-up -outseq Athaliana_167_TAIR9_EmbossShuffled.fas<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Strangely, in the output file, the fasta headers were all repetitive Chr1.<o:p></o:p></p>
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<p class="MsoNormal">Hence my confusion. Could someone please clarify what my input formatting should be and the correct syntax?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Thanks, in advance, for your help.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Sincerely,<o:p></o:p></p>
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<p class="MsoNormal">Anand<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;color:#500050">_____</span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;color:blue">Anand</span></b><b><span style="font-size:7.5pt;color:red">k</span></b><span style="font-size:7.5pt;color:#500050">umar </span><b><span style="font-size:7.5pt;color:red">S</span></b><span style="font-size:7.5pt;color:#500050">urendra</span><b><span style="font-size:7.5pt;color:blue">rao</span></b><span style="font-size:7.5pt;color:#500050">,
PhD</span><span style="color:#500050"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:7.5pt;color:#500050">+<span class="gmail-m1109981565332667423gmail-il">1.530</span>.<span class="gmail-m1109981565332667423gmail-il">574.5134</span></span><span style="color:#500050"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:7.5pt;color:#500050">+91.91760.70887</span><span style="color:#500050"><o:p></o:p></span></p>
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