<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Susan<div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 11 Jul 2016, at 16:45, 梁薰文 <<a href="mailto:a24681012142002@gmail.com" class="">a24681012142002@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html charset=big5" class=""><div 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></div></div></blockquote><div><br class=""></div><div><br class=""></div><div>At present we offer access to bacterial annotation as submitted to the ENA/GenBank/DDBJ archives. For 30,000 species, we cannot judge the merits of rival annotations in individual cases. It is possible that we might switch to using the RefSeq-provided annotations at some point in future, but there are not presently plans to do this.</div><div><br class=""></div><div>best wishes,</div><div><br class=""></div><div>Paul</div><div><br class=""></div><br class=""><blockquote type="cite" class=""><div class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><div class=""><br class=""></div><div class=""><font class="">Last time you also mentioned "origin-spanning features”, but I only found this on google.</font></div><div class=""><font class="">It’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 class=""><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=""></div>_______________________________________________<br class="">Dev mailing list <a href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a><br class="">Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" class="">http://lists.ensembl.org/mailman/listinfo/dev</a><br class="">Ensembl Blog: <a href="http://www.ensembl.info/" class="">http://www.ensembl.info/</a><br class=""></div></blockquote></div><br class=""><div class="">
<div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-variant-ligatures: normal; font-variant-position: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; line-height: normal; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><br class="Apple-interchange-newline">---</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-variant-ligatures: normal; font-variant-position: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; line-height: normal; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dr. Paul Kersey</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-variant-ligatures: normal; font-variant-position: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; line-height: normal; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Team Leader, Non-vertebrate Genomics</div><div class="">European Bioinformatics Institute</div><div class="">European Molecular Biology Laboratory Tel: +44-(0)1223-494601</div><div class="">Wellcome Genome Campus, Hinxton Fax: +44-(0)1223-494468<br class="">Cambridge CB10 1SD, UK email: <a href="mailto:pkersey@ebi.ac.uk" class="">pkersey@ebi.ac.uk</a><br class=""><br class=""><br class=""></div></div>
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