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<p class=MsoNormal>Dear Colleagues,<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I am just learning how to use SeqinR and it looks extremely useful.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I am trying to figure out how I can use SeqinR to query the
genbank database to get the sequence corresponding to a particular accession
number, but am having a problem.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>For example, the accession number corresponding to the
Bacteriophage lambda genome is NC_001416.<o:p></o:p></p>
<p class=MsoNormal>I tried to get this sequence by typing in R:<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l2 level1 lfo3'><![if !supportLists]><span
style='font-family:Wingdings'><span style='mso-list:Ignore'>Ų<span
style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>library(“seqinr”)<o:p></o:p></p>
<p class=MsoListParagraph><o:p> </o:p></p>
<p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l2 level1 lfo3'><![if !supportLists]><span
style='font-family:Wingdings'><span style='mso-list:Ignore'>Ų<span
style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>choosebank(“genbank”)<o:p></o:p></p>
<p class=MsoListParagraph><o:p> </o:p></p>
<p class=MsoListParagraph><o:p> </o:p></p>
<p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l2 level1 lfo3'><![if !supportLists]><span
style='font-family:Wingdings'><span style='mso-list:Ignore'>Ų<span
style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>query(“lambda”,”AC=NC_001416”)<o:p></o:p></p>
<p class=MsoListParagraph><o:p> </o:p></p>
<p class=MsoNormal>The first two commands work fine, however, I get this error
message from the query command:<o:p></o:p></p>
<p class=MsoNormal> Error in query("lambda",
"AC=NC_000907") : <o:p></o:p></p>
<p class=MsoNormal> invalid request:"unknown accession number at (^):
\"AC<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I am not sure what I am doing wrong, as other requests are
working fine for me, eg. the command<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l2 level1 lfo3'><![if !supportLists]><span
style='font-family:Wingdings'><span style='mso-list:Ignore'>Ų<span
style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>query("lambda","AC=CP001252")<o:p></o:p></p>
<p class=MsoListParagraph><o:p> </o:p></p>
<p class=MsoNormal>works fine for me.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Does anyone know what I am doing wrong?<o:p></o:p></p>
<p class=MsoNormal>I will be very grateful for any advice you can give.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Regards,<o:p></o:p></p>
<p class=MsoNormal>Avril <o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Avril Coghlan<o:p></o:p></p>
<p class=MsoNormal>Department of Microbiology<o:p></o:p></p>
<p class=MsoNormal>University College Cork<o:p></o:p></p>
<p class=MsoNormal>Ireland<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
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