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<TITLE> [Refseq-announce] Important reminder of upcoming RefSeq FTP changes
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<H1>[Refseq-announce] Important reminder of upcoming RefSeq FTP changes</H1>
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<B>Public RefSeq Release announcements</B>
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<A HREF="mailto:refseq-announce%40ncbi.nlm.nih.gov?Subject=Re%3A%20%5BRefseq-announce%5D%20Important%20reminder%20of%20upcoming%20RefSeq%20FTP%20changes&In-Reply-To=%3Cmailman.188833.1397770972.8578.refseq-announce%40ncbi.nlm.nih.gov%3E"
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TITLE="[Refseq-announce] Important reminder of upcoming RefSeq FTP changes">refseq-announce at ncbi.nlm.nih.gov
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</A><BR>
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<I>Thu Apr 17 17:42:39 EDT 2014</I>
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<P><UL>
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<LI>Next message: <A HREF="000118.html">[Refseq-announce] Announcing RefSeq release 65
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<PRE>Please note that several changes to the RefSeq release FTP site will occur with RefSeq release 65, planned for early May. These changes were indicated in previous release announcements.
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1. Directory name change: The 'microbial' directory will be removed. Two new directories 'archaea' and 'bacteria' will be added.
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2. WGS management change: WGS accessions will no longer be processed on a per-project (WGS prefix) basis. Instead, these accessions will be processed and packaged the same as non-WGS accessions. This will significantly reduce the number of files in the /complete/ and (new) /archaea/ and /bacteria/ directories. Therefore, there will no longer be a series of files named like 'microbialNZ_*'. Instead, all WGS scaffolds will be found in concatenated files just like all other accession data. We will continue to provide a separate file for the WGS master records.
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Please note that this change in WGS management will also impact the /refseq/daily/ and /refseq/wgs/ directory areas. This impact was not spelled out in previous emails. As WGS accessions are processed the same as other non-WGS accessions, these updates will now appear in the /daily/ update area. WGS master records will continue to be provided separately from other files as they are special meta-data only records. WGS mater files will be provided with names like 'rsnc.wgs_mstr.0403.2014.bna.gz' and 'rsnc.wgs_mstr.0403.2014.gbff.gz' (where "wgs_mstr" indicates the type). These files will be provided in the /refseq/wgs/ directory area.
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3. File name & Content change:
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This change will occur in both /refseq/daily/ and /refseq/release/release-catalog/ directory areas
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*WP2genomic.mapping.gz will be renamed *AutonomousProtein2Genomic.gz
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*multispecies_WP_accession_to_taxname.gz will be renamed *MultispeciesAutonomousProtein2taxname.gz
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Both file names will be modified in order to more accurately reflect the terminology that is being used to refer to the autonomous nonredundant protein dataset that utilizes the 'WP_' accession prefix. In addition, the content of the AutonomousProtein2Genomic file will be expanded to include:
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* protein accession.version
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* protein gi
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* genomic accession.version (on which the autonomous WP protein is annotated)
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* genomic gi
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* genomic annotated strain-level taxid
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* genomic species-level taxid
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* genomic BioSample ID if available
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* genomic organism name (e.g., species + strain)
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Kim D. Pruitt, Ph.D
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NCBI/NLM/NIH/DHHS
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45 Center Drive
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Building 45 Room 4AS47B MSC 6513
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Bethesda, MD 20892-6513
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Phone (301)435-5898
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Please consider the environment before printing this e-mail.
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</PRE>
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