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Dear Ran Wei,<br>
<br>
the problem is related to the fact that there are refseq "partitions" for different type of data, as you can see on the ftp which is where we get the data for indexing acnuc databases<br>
<p><a href="ftp://ftp.ncbi.nlm.nih.gov/refseq/release/" target="_blank">ftp://ftp.ncbi.nlm.nih.gov/refseq/release/</a></p>
<p><br>
</p>
<p>We do not index all these partitions, but maybe we should do it in the future (not before October however).</p>
<p>The current acnuc database called RefSeq contains RNA refseq sequence.</p>
<p><br>
</p>
<p><br>
</p>
<p></p>
<p>However you can access to your RefSeq sequence in Genbank, when the sequence derives from Genbank.
</p>
<p><br>
</p>
<p>There must be several ways to do it but for your example:</p>
<p><br>
</p>
<p><font size="2"><span style="font-size:10pt"><a href="https://www.ncbi.nlm.nih.gov/nuccore/NC_001477">https://www.ncbi.nlm.nih.gov/nuccore/NC_001477</a></span></font></p>
<p><font size="2"><span style="font-size:10pt"><br>
</span></font></p>
<p><font size="2"><span style="font-size:10pt"><br>
</span></font></p>
<p><font size="2"><span style="font-size:10pt"><span style="font-size: 12pt;">you can find in the COMMENTS fields the accession number of the Genbank sequence : U88536
</span><br>
</span></font></p>
<p><font size="2"><span style="font-size:10pt"><a href="https://www.ncbi.nlm.nih.gov/nuccore/U88536">https://www.ncbi.nlm.nih.gov/nuccore/U88536</a><br>
</span></font></p>
<p><font size="2"><span style="font-size:10pt"><br>
</span></font></p>
<p><font size="2"><span style="font-size:10pt"><br>
</span></font></p>
<p><font size="2"><span style="font-size:10pt"><font size="2"><span style="font-size:10pt"><span style="font-size: 12pt;">with seqinr:</span></span></font><br>
</span></font></p>
<p><font size="2"><span style="font-size:10pt"><br>
</span></font></p>
<p><font size="2"><span style="font-size:10pt">> choosebank("genbank")<br>
</span></font></p>
<p><font size="2"><span style="font-size:10pt">> lambda <- query("lambda","AC=U88536")<br>
</span></font></p>
<p><font size="2"><span style="font-size:10pt">>myseq <-getSequence(lambda)<br>
</span></font></p>
<p><font size="2"><span style="font-size:10pt"><span style="font-size: 12pt;"><br>
</span></span></font></p>
<p><font size="2"><span style="font-size:10pt"><span style="font-size: 12pt;"><br>
</span></span></font></p>
<p><font size="2"><span style="font-size:10pt"><span style="font-size: 12pt;">Note: be carefull that you should give the same name to the list in the query and to the results of the query<br>
</span></span></font></p>
<p><font size="2"><span style="font-size:10pt"><span style="font-size: 12pt;"><br>
</span></span></font></p>
<p><font size="2"><span style="font-size:10pt"><span style="font-size: 12pt;">I think there are cross reference files between Genbank and Refseq, you may find some information here</span><br>
<a href="ftp://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt" target="_blank">ftp://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt</a><br>
<br>
</span></font>I hope this help a little<br>
</p>
<p>all the best</p>
<p><br>
</p>
<p>Simon</p>
<p><br>
</p>
<p><br>
</p>
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<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" color="#000000" face="Calibri, sans-serif"><b>De :</b> seqinr-forum-bounces@lists.r-forge.r-project.org <seqinr-forum-bounces@lists.r-forge.r-project.org> de la part de Ran Wei <weira@njms.rutgers.edu><br>
<b>Envoyé :</b> lundi 7 août 2017 21:08<br>
<b>À :</b> seqinr-forum@lists.r-forge.r-project.org<br>
<b>Objet :</b> [Seqinr-forum] Seqinr</font>
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<p class="MsoNormal">Hello all,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">I am new to seqinr. Today I was trying to connect to the genbank database and send queries. It worked well for some sequences:</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">> choosebank("genbank")</p>
<p class="MsoNormal">> query("lambda","AC=CP001252")</p>
<p class="MsoNormal">> mylambda <- get("lambda",env=.seqinrEnv)</p>
<p class="MsoNormal">> attributes(mylambda)</p>
<p class="MsoNormal">$names</p>
<p class="MsoNormal">[1] "call" "name" "nelem" "typelist" "req" "socket"
</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">$class</p>
<p class="MsoNormal">[1] "qaw"</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">However, for a set of other sequences an error was thrown:</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">> query("dengue1", "AC=NC001477")</p>
<p class="MsoNormal">Error in query("dengue1", "AC=NC001477") : </p>
<p class="MsoNormal"> invalid request:"unknown accession number at (^): \"AC</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">And not only accession number, using other parameters also incurs error:</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">> query('naturepaper', 'R=Nature/460/352')</p>
<p class="MsoNormal">Error in query("naturepaper", "R=Nature/460/352") : </p>
<p class="MsoNormal"> invalid request:"unknown reference at (^): \"R</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">In addition, I also found that not all databases could be loaded:</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">> choosebank("refseqViruses")</p>
<p class="MsoNormal">Error in acnucopen(bank, socket) : </p>
<p class="MsoNormal"> Database with name -->refseqViruses<-- is not known by server.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Could anyone let me know how should I fix these problems? Version of this seqinr package is 3.3-6, running under 64-bit R in Win10 system.
</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Thank you and best regards,</p>
<p class="MsoNormal">Ran Wei </p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"> </p>
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