<html><head><meta http-equiv="Content-Type" content="text/html charset=big5"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><div class=""><font class="">Hi Dan,<br class=""><br class="">We are importing thirteen<i class=""> Klebsiella pneumonia</i> strains, one of them is PMK1(ASM76461v1).<br class="">After your noticing, I indeed found those genomes existing in EnsemblBacteria.</font></div><div class=""><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div class=""><div class=""><font class="">However, I noticed that NCBI RefSeq provides updates to the annotation of the genomes of these strains.</font><span class=""> </span></div></div></div></div><div class=""><font class=""><font class="">The mainly difference between RefSeq and GenBank assembly lies in the feature annotation and its number, such as gene number and protein number. Here are predicted number of PMK1 in GenBank and RefSeq assembly:</font></font></div><div class=""><font class=""><span class="Apple-tab-span" style="white-space:pre"> </span>a. GenBank version: 5,705 genes, </font><span style="white-space: pre-wrap; widows: 1; background-color: rgb(255, 255, 255);" class="">5,594</span> proteins</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>b. RefSeq version: 5,879 genes, 5,672 proteins</div><div class=""><br class=""><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div class=""><font class="">Below lists detailed information of PMK1 strain as reference. (NCBI refseq URL: <a href="http://www.ncbi.nlm.nih.gov/refseq/" class="">http://www.ncbi.nlm.nih.gov/refseq/</a>)</font></div></div><ul class="MailOutline"><li class=""><font class="">Strain: PMK1 (direct URL to the assembly record <a href="http://www.ncbi.nlm.nih.gov/assembly/GCA_000764615.1" class="">http://www.ncbi.nlm.nih.gov/assembly/GCA_000764615.1</a>)</font></li><li class=""><font class="">GenBank assembly accession: GCA_000764615.1 (latest) </font></li><ul class=""><li class=""><font class="">gb file URL: <a href="ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000764615.1_ASM76461v1/GCA_000764615.1_ASM76461v1_genomic.gbff.gz" class="">ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000764615.1_ASM76461v1/GCA_000764615.1_ASM76461v1_genomic.gbff.gz</a></font></li></ul><li class=""><font class="">RefSeq assembly accession: GCF_000764615.1 (latest)</font></li><ul class=""><li class=""><font class="">gb file URL: <a href="ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000764615.1_ASM76461v1/GCF_000764615.1_ASM76461v1_genomic.gbff.gz" class="">ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000764615.1_ASM76461v1/GCF_000764615.1_ASM76461v1_genomic.gbff.gz</a></font></li></ul></ul></div><div class=""><br class=""></div><div class=""><font class="">Last time you also mentioned "origin-spanning featuresˇ¨, but I only found this on google.</font></div><div class=""><font class="">Itˇ¦s one of the ensembl-dev topics in 2005.<br class="">Please tell me if I find wrong.<br class=""><a href="http://dev.ensembl.narkive.com/9KWpLOT4/circular-sequences" class="">http://dev.ensembl.narkive.com/9KWpLOT4/circular-sequences</a><br class=""><br class="">Thanks very much for your help and improve our code.<br class="">Please find it in the attachment.<br class=""><br class=""></font><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div class=""><div class=""><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div class=""><font class="">Susan</font></div></div></div></div></div></div></div><div class=""><br class=""></div><br class=""><div><blockquote type="cite" class=""><div class="">On Jul 7, 2016, at 4:52 PM, Dan Staines <<a href="mailto:dstaines@ebi.ac.uk" class="">dstaines@ebi.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi Susan,<br class=""><br class="">Ensembl does support origin-spanning features - we have these in Ensembl<br class="">Bacteria. Can you please share with me a small piece of code showing how<br class="">you are storing the data so we can see what the problem might be?<br class=""><br class="">Out of interest, which prokaryotic genomes are you importing? There are<br class="">over 40,000 in Ensembl Bacteria which come from EMBL/GenBank so its<br class="">possible that the genomes you are interested in are already present.<br class=""><br class="">Thanks,<br class=""><br class="">Dan.<br class=""><br class="">-- <br class="">Dan Staines, PhD<br class="">Genomics Technology Infrastructure Coordinator<br class="">EMBL-EBI, Wellcome Trust Genome Campus<br class="">Cambridge CB10 1SD, UK<br class="">Tel: +44-(0)1223-492507<br class=""></div></div></blockquote></div><br class=""></body></html>