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README for ftp://ftp.ncbi.nih.gov/refseq/{species-specific}

Last updated: May 23, 2018
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_________________________________________________________________________
       National Center for Biotechnology Information (NCBI)
             National Library of Medicine
             National Institutes of Health
             8600 Rockville Pike
             Bethesda, MD 20894, USA
             tel: (301) 496-2475
             fax: (301) 480-9241
             e-mail: info@ncbi.nlm.nih.gov            
_________________________________________________________________________

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UPDATES TO THIS FTP SITE AND README:

March 10, 2008
      Added documentation for H_sapiens/RefSeqGene/
      Minor formatting modifications

November 17, 2014
      Documented file name format change 
      Files include incremental file number information following size-
      based split.
      Additional minor formatting modifications

November 25, 2014
      Availability of file list for species-specific mRNA_Prot directories

September 18, 2017
      Changed weekly update day from Monday to Tuesday

May 23, 2018
      Updated the ABOUT section to clarify the description of the contents
      of the species-specific RefSeq directories
      
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==============
ABOUT:
==============

The species-specific RefSeq directories provide the complete current set of records for
transcripts and proteins for those species, and includes all RefSeq accessions (and versions)
available for the organism as of the date the file was created. Note that model XM_, XR_, and
XP_ accessions are included in addition to the known RefSeq complement with NM_, NR_, and NP_
accessions. 
 
The transcripts and proteins in these files represent the most up-to-date versions of theRefSeq
accessions, and differ from the contents of the genome annotation transcript and protein files
(ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/), which represent a static set of
products that were annotated at a particular point in time, i.e., at the time of the most recent
Annotation Release.

These directories are updated on a weekly basis; the update is typically
installed on Tuesdays:
ftp://ftp.ncbi.nlm.nih.gov/refseq/B_taurus/
ftp://ftp.ncbi.nlm.nih.gov/refseq/D_rerio/
ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/
ftp://ftp.ncbi.nlm.nih.gov/refseq/M_musculus/
ftp://ftp.ncbi.nlm.nih.gov/refseq/R_norvegicus/
ftp://ftp.ncbi.nlm.nih.gov/refseq/S_scrofa/
ftp://ftp.ncbi.nlm.nih.gov/refseq/X_tropicalis/

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SUB-DIRECTORIES:
==========================

{SPECIES_ABBREV}: a link to related FTP area where the genome, genome annotation,
	          and genome assembly sequence reports are provided.

mRNA_Prot directory
   Contents: organisms-specific RefSeq transcript and protein data

     {org-name}.files.installed: 
         reports the md5checksum and files included in the directory
         For example: /refseq/H_sapiens/mRNA_Prot/human.files.installed

   File Name Conventions:
	File name formats are as follows:
 	     common_name.#.molecule_type.format_type
        Multiple files may be provided for any given molecule and format type and file 
	names include a numerical increment.  Files with the same numerical increment
	are related by content. 

	For example, the files provided for human are named as:
 	      human.#.rna.fna.gz --fasta report for transcript records
 	      human.#.protein.faa.gz --fasta report for protein records
 	      human.#.rna.gbff.gz  --flatfile report for transcript records
 	      human.#.protein.gpff.gz --flatfile report for protein records

RefSeqGene directory:   
   genomic gene-region sequence data that is provided to support the RefSeqGene project 
   and Clinical Testing labs. Genomic records in scope for reporting to this FTP 
   directory can be identified by the presence of the keyword 'RefSeqGene'.
	     
   Available in: H_sapiens directory
   See also:  http://www.ncbi.nlm.nih.gov/refseq/RSG/ 
   Files provided:
	 gene_RefSeqGene -- a gene-to-accession mapping file 
		            tab delimited columns are 
		            tax_id GeneID symbol NG_accession.version	        
	 LRG_RefSeqGene  -- a LRG to RefSeqGene mapping file
		            tab delimited columns are
		            GeneID  symbol  LRG_ID RefSeqGene accession.version
	 RefSeqGene#.genomic.molecule_type.format_type --sequence reports; see above
	 RefSeqGene_standards -- reports genomic and transcript reference standards
				        tab delimited columns are
					GeneID   symbol  NG or NM accession.version
                                        # Note NG = genomic; NM = transcript 
	README_SUBMIT
 	   SubmittingVariationHelp.pdf
	   submission_template.xls			

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Disclaimer:
==========================
The United States Government makes no representations or warranties
regarding the content or accuracy of the information.  The United States
Government also makes no representations or warranties of merchantability
or fitness for a particular purpose or that the use of the sequences will
not infringe any patent, copyright, trademark, or other rights.  The
United States Government accepts no responsibility for any consequence
of the receipt or use of the information.

For additional information about RefSeq releases, please contact
NCBI by e-mail at info@ncbi.nlm.nih.gov or by phone at (301) 496-2475.