From jorvis at gmail.com Thu May 8 15:33:45 2008 From: jorvis at gmail.com (Joshua Orvis) Date: Fri May 9 12:00:46 2008 Subject: [Ixodes] Ixodes ID mapping file Message-ID: The ID mapping file provided on your website has entries like this: internal id GenBank accession ============= ================= 1106618050105 DS611849 But these numbers to not match the entries within the accessions on GenBank, for example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=183976674 LOCUS DS611849 1067 bp DNA linear CON 18-APR-2008 DEFINITION Ixodes scapularis 1108376228926 genomic scaffold, whole genome shotgun sequence. Is it possible to provide a file that links the DS* IDs with the newer ones that start with 1108? Thanks - JO -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.vectorbase.org:82/pipermail/iscapularis/attachments/20080508/23849e98/attachment-0001.html From mhammond at ebi.ac.uk Fri May 9 12:18:38 2008 From: mhammond at ebi.ac.uk (Martin Hammond) Date: Fri May 9 12:19:13 2008 Subject: [Ixodes] Ixodes ID mapping file In-Reply-To: References: Message-ID: <8810C3CC-7790-46D3-8935-E6E71D2D5DB9@ebi.ac.uk> Hi Joshua, At VectorBase, we previously made the scaffolds available with the 'internal' scaffold identifiers then in use at JCVI (these started with 1106). At that time there were no other identifiers available and it was hoped that there would be no other identifiers in use until scaffolds were accessioned in GenBank. However, JCVI did then switch to a new set of internal identifiers starting 1108. These have never been visible at VectorBase, so we would prefer not to confuse people by putting up a look-up file for them. I note that the 1108... JCVI internal ids appear in the Definition line of GenBank scaffold entries (as in your example), so the correspondance can be obtained from the GenBank entries. But I do already have such a file, and will email it to you separately. Regards, Martin Martin Hammond VectorBase / EBI On 8 May 2008, at 20:33, Joshua Orvis wrote: > The ID mapping file provided on your website has entries like this: > > internal id GenBank accession > ============= ================= > 1106618050105 DS611849 > > But these numbers to not match the entries within the accessions on > GenBank, for example: > > http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=183976674 > > LOCUS DS611849 1067 bp DNA linear CON 18-APR-2008 > DEFINITION Ixodes scapularis 1108376228926 genomic scaffold, whole > genome > shotgun sequence. > Is it possible to provide a file that links the DS* IDs with the > newer ones that start with 1108? > > Thanks - > > JO > _______________________________________________ > Iscapularis mailing list > Iscapularis@vectorbase.org > http://mail.vectorbase.org:82/mailman/listinfo/iscapularis