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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link="#0563C1" vlink="#954F72"><div class=WordSection1><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Calibri",sans-serif'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Calibri",sans-serif'>Hi, guys:<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Calibri",sans-serif'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Calibri",sans-serif'>Previously I have been using library(Biostrings). <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Calibri",sans-serif'>For example, I have used the following 2 lines to read in a SARS-COV-2 FASTA file and find the positions for all “A” allele.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Calibri",sans-serif'> <span style='background:yellow;mso-highlight:yellow'>fa <- readDNAStringSet(“MY-FASTA.fa”, format="fasta")<o:p></o:p></span></span></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Calibri",sans-serif;background:yellow;mso-highlight:yellow'> I could then use vmatchPattern("A", fa, max.mismatch=0)</span><span style='font-size:12.0pt;font-family:"Calibri",sans-serif'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Calibri",sans-serif'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Calibri",sans-serif'>However, the output from the above vmatchPattern() command is a bit messy. <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Calibri",sans-serif'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Calibri",sans-serif'>I wish that SeqinR package could do this more straight-forward.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Calibri",sans-serif'>If so, can someone please let me know how to write my above Biostrings command for SeqinR?<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Calibri",sans-serif'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Calibri",sans-serif'>Thank you very much & best regards,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Calibri",sans-serif'>Jie<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>