********************************************************************************
RefSeq-release69.txt       ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-notes/

		NCBI Reference Sequence (RefSeq) Database

			Release 69
			January 2, 2015

		Distribution Release Notes

Release Size: 
51661 organisms, 594452675642 nucleotide bases, 18690872100 amino acids, 74127019 records
******************************************************************************

This document describes the format and content of the flat files that 
comprise releases of the NCBI Reference Sequence (RefSeq) database.

Additional information about RefSeq is available at:

1. NCBI Bookshelf:
   a) NCBI Handbook:  
   http://www.ncbi.nlm.nih.gov/books/NBK21091/
   b) RefSeq Help (FAQ)
   http://www.ncbi.nlm.nih.gov/books/NBK50680/
 
2. RefSeq Web Sites: 
   RefSeq Home:  http://www.ncbi.nlm.nih.gov/RefSeq/
   RefSeqGene Home: http://www.ncbi.nlm.nih.gov/refseq/rsg/

If you have any questions or comments about RefSeq, the RefSeq release files
or this document, please contact NCBI by email at:
   info@ncbi.nlm.nih.gov. 

To receive announcements of future RefSeq releases and large updates please
subscribe to NCBI's refseq-announce mail list:

 send email to refseq-announce-subscribe@ncbi.nlm.nih.gov
 with "subscribe" in the subject line (without quotes)
 and nothing in the email body

OR

 subscribe using the web interface at:
 http://www.ncbi.nlm.nih.gov/mailman/listinfo/refseq-announce

=============================================================================
TABLE OF CONTENTS
=============================================================================
1. INTRODUCTION	
	1.1 Release 69
	1.2 Cutoff date
	1.3 RefSeq Project Background
		1.3.1 Sequence accessions, validation, and annotations
		1.3.2 Data assembly, curation, and collaboration 
		1.3.3 Biologically non-redundant data set
		1.3.4 RefSeq and DDBJ/EMBL/GenBank comparison
	1.4 Uses and applications of the RefSeq database
2. CONTENT
	2.1 Organisms included
	2.2 Molecule Types included
	2.3 Known Problems, Redundancies, and Inconsistencies
	2.4 Release Catalog
	2.5 Changes since the previous release 
3. ORGANIZATION OF DATA FILES
	3.1 FTP Site Organization
	3.2 Release Contents
	3.3 File Names and Formats
        3.4 File Sizes
        3.5 Statistics
	3.6 Release Catalog
	3.7 Removed Records
      	3.8 Accession Format
        3.9 Growth of RefSeq        
4. FLAT FILE ANNOTATION
	4.1 Main features of RefSeq Flat File
		4.1.1 LOCUS, DEFLINE, ACCESSION, KEYWORDS, SOURCE, ORGANISM
		4.1.2 REFERENCE, DIRECT SUBMISSION, COMMENT
		4.1.3 FEATURE ANNOTATION (Gene, mRNA, CDS, Variation, Protein)
	4.2 Tracking Identifiers
		4.2.1 GeneID
		4.2.2 Transcript ID
		4.2.3 Protein ID
		4.2.4 Conserved Domain Database (CDD) ID
5. REFSEQ ADMINISTRATION
	5.1 Citing RefSeq
	5.2 RefSeq Distribution Formats
	5.3 Other Methods of Accessing RefSeq Data
	5.4 Request for Corrections and Comments
	5.5 Credits and Acknowledgements
	5.6 Disclaimer

=============================================================================
1. INTRODUCTION
=============================================================================
The NCBI Reference Sequence Project (RefSeq) is an effort to provide the 
best single collection of naturally occurring biomolecules, representative
of the central dogma, for each major organism. Ideally this would include 
one sequence record for each chromosome, organelle, or plasmid linked on a 
residue by residue basis to the expressed transcripts, to the translated 
proteins, and to each mature peptide product. Depending on the organism, we 
may have some, but not all, of this information at any given time. We 
pragmatically include the best view we can from available data.

Additional information about the RefSeq project is available from:
   a) RefSeq Web site  
      http://www.ncbi.nlm.nih.gov/refseq/
   b) Entrez Books, NCBI Handbook, RefSeq chapter
      http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=handbook.chapter.ch18

1.1 Release 69
--------------
The National Center for Biotechnology Information (NCBI) at the National
Library of Medicine (NLM), National Institutes of Health (NIH) is 
responsible for producing and distributing the RefSeq Sequence Database. 
Records are provided through a combination of collaboration and in-house 
processing including some curation by NCBI staff comprised of expert 
biologists.  

This is a full release of all NCBI RefSeq records.
The RefSeq project is an ongoing effort to provide a curated, non-redundant
collection of sequences. This release includes all of the sequence data
that we have collected at this time. Although the RefSeq collection is not yet 
complete, its value as a non-redundant dataset has reached a level that
justifies providing full releases.  

1.2 Cutoff date
---------------
This full release, release 69, incorporates data available as of
January 2, 2015.

For more recent data, users are advised to:
	
   1. Download the RefSeq daily update files from the RefSeq FTP site
      ftp://ftp.ncbi.nlm.nih.gov/refseq/daily/

   2. Use NCBI's Entrez Programming Utilities to download records
      based on queries or lists of accessions
      http://www.ncbi.nlm.nih.gov/books/NBK25500/

   3. Use the interactive web query system to query based on date.
      http://www.ncbi.nlm.nih.gov/nucleotide/
      http://www.ncbi.nlm.nih.gov/protein/

1.3 RefSeq Project Background
-----------------------------

1.3.1 Sequence accessions, validation, and annotation
-----------------------------------------------------
Every sequence is assigned a stable accession, version, and gi and 
all older versions remain available over time. RefSeq accessions
have a distinct format (see section 3.6); the underscore ("_") is the 
primary distinguishing feature of a RefSeq accession. 
DDBJ/EMBL/GenBank accessions never include an underscore.

Sequences are validated in several ways. For example, to confirm 
that genomic sequence from the region of the mRNA feature really 
does match the mRNA sequence itself, and that the annotated coding region 
features really can be translated into the protein sequences they refer to.
Validation also checks for valid ASN.1 format. Validation also ensures that
consistency is maintained in descriptive information (symbols, gene and 
protein names) between RefSeq and Gene records.

Each molecule is annotated as accurately as possible with the 
correct organism name, the correct gene symbol for that organism, 
and reasonable names for proteins where possible. When available, 
nomenclature provided by official nomenclature groups is used.  
Note that gene symbols are not required or expected to be unique 
either across species or within a species. 

1.3.2 Data assembly, curation, and collaboration 
------------------------------------------------
We welcome collaborations with authoritative groups outside NCBI 
who are willing to provide the sequences, annotations, or links 
to phenotypic or organism specific resources. Where such collaborations 
have not yet developed, NCBI staff have assembled the best view of 
the organism that we can put together ourselves. In some cases, as with the 
human genome, NCBI is an active participant in generating the 
genome assembly and in providing reference sequences to represent 
the annotated genome. For other genomes, we may compile the data 
ourselves from DDBJ/EMBL/GenBank or other public sources. For instance,  
we may simply select the "best" DDBJ/EMBL/GenBank record by automatic means, 
validate the data format (and correct if needed), and add an essentially 
unchanged copy to the RefSeq collection, attributed to the original 
DDBJ/EMBL/GenBank record. In other cases we may provide a record that is very 
similar to the DDBJ/EMBL/GenBank record, but to which experts at NCBI have added 
corrected or additional annotation. This latter process can range 
from minor technical repairs to a manually curated re-annotation of 
the sequence, often in collaboration with experts outside NCBI. 

Each record that has been curated, or that is in the pool for
future curation, is labeled with the level of curation it has received.  
Curation status information is provided primarily for transcript and 
protein records.  Curation is carried out on the whole genome level 
for some smaller genomes such as viral, organelle, and some microbial
genomes.  

Curation status codes are defined in the section 3.2 below.

1.3.3 Biologically non-redundant data set
-----------------------------------------
RefSeq provides a biologically non-redundant set of sequences for database 
searching and gene characterization. It has the advantage of providing an 
objective and experimentally verifiable definition of "non-redundant" in 
supplying one example of each natural biomolecule per organism or sample.
The small amount of sequence redundancy introduced from close paralogs,
alternate splicing products, and genome assembly intermediates is compensated
for by the clarity of the model. RefSeq provides the substrate for a variety
of conclusions about non-redundancy based on clustering identical sequences, 
or families of related sequences, without confounding the database itself 
with these more subjective assessments.

1.3.4 RefSeq and DDBJ/EMBL/GenBank comparison
---------------------------------------------
RefSeq is unique in providing a large curated database across many 
organisms, which precisely and explicitly links genetic (chromosome), 
expression (mRNA), and functional (protein) sequence data into an 
integrated whole. 

DDBJ/EMBL/GenBank also integrates DNA and protein information, and RefSeq is 
substantially based on sequence records contributed to DDBJ/EMBL/GenBank. 
However, RefSeq is similar to a review article in that it represents 
a synthesis and summary of information by a particular group (NCBI or 
other RefSeq contributors) that is based on the primary data gathered 
by many others and made part of the scientific record. Also, like a 
review article, it has the advantage of organizing a large body of 
diverse data into a single consistent framework with a uniform set of 
conventions and standards.

Note that while based on DDBJ/EMBL/GenBank, RefSeq is distinct from 
DDBJ/EMBL/GenBank. DDBJ/EMBL/GenBank represents the sequence and annotations 
supplied by the original authors and is never changed by NCBI or RefSeq staff. 
DDBJ/EMBL/GenBank remains the primary sequence archive while RefSeq is a 
summary and synthesis based on that essential primary data.

1.4 Uses and applications of the RefSeq database
------------------------------------------------
A stable, consistent, comprehensive, non-redundant database of genomes
and their products provides a valuable sequence resource for similarity 
searching, gene identification, protein classification, comparative 
genomics, and selection of probes for gene expression. It also acts as 
molecular "white pages" by providing a single, uniform point of access 
for searching at the sequence level, and by connecting the results with 
a diversity of organism-specific databases or resources unique to that 
organism or field. 

=============================================================================
2. CONTENT
=============================================================================
2.1 Organisms included
----------------------
This number of organisms reported for the release (section 3.5 below) is 
determined by counting the number of distinct tax_ids included in the release.
Tax_ids are provided by the NCBI Taxonomy group. Tax_ids were historically 
provided for all species and strains having any amount of sequence data. In 2014
NCBI stopped assigning strain-level tax_ids. Strains are now being tracked by
the BioSample database.  

The release includes species ranging from viral to microbial to eukaryotic and 
includes organisms for which complete and incomplete genomic sequence data is 
available.  

The release does not include all species for which some sequence data is
available in DDBJ/EMBL/GenBank. The decision to generate RefSeq data for a 
species or strain depends in part on the amount of sequence data available.  
Additional species will be represented in the RefSeq collection as more
sequence data becomes available.

2.2 Molecule Types Included
---------------------------
The RefSeq release includes genomic, transcript, and protein sequence data; 
however, these molecule types are not provided for all organisms and the 
sequences provided may not be complete or comprehensive for some species.  

Transcript RefSeq records may represent protein-coding transcripts or 
non-coding RNA products; these records are currently only provided for 
eukaryotic species.

Genomic RefSeq records are provided when a sufficient quantity of genomic 
sequence data is available in DDBJ/EMBL/GenBank. Transcript and protein 
records may be provided for a species before genomic sequence data is available.

2.3 Known Problems, Redundancies, and Inconsistencies
------------------------------------------------------

Known Problems with RefSeq release 69:
======================================
NC_023641.1 and YP_009010973 are not included in the release due to an identified
error in the molecule type information for NC_023641.1. The molecule type 'mRNA' is
not valid for the accession prefix 'NC_'; this error was corrected after RefSeq 
release processing completed.


Known Redunancies and Inconsistencies:
======================================
The RefSeq collection is an ongoing project that is expected to grow
in scope and content over time.  Thus it is important to recognize that
it is not complete in that some genomes are not yet completely sequenced,
some incompletely sequenced genomes may not be included, or some gene 
products may not yet be represented. RefSeq records may be added, removed, 
or updated in future releases as new information becomes available and as 
a result of curation.

Known Data inconsistencies:

	[1] RefSeq status codes are not consistently provided for some species. 
	The goal is to consistently provide a status code for all RefSeq
	records. The release catalog indicates "UNKNOWN" if a status code
	was expected but not detected and "na" if a status code is not
	expected based on the original project plan for provision of this type
	of information. Status codes will be more consistently applied to all 
	records in the future.

	[2] The genomic, transcript, and protein collection is known to be 
	incomplete for many species. This is particularly true for those
	genomes for which a complete genome assembly is not yet available, 
	such as Sus scrofa (pig). As additional sequence data becomes available, 
	the RefSeq representation for this, and other, organisms will increase. 
	
	[3] Whole genome shotgun (WGS) assemblies of organelle, plastid, or viral genomes 
	are included in the complete node and in the taxonomic group that the 
	whole genome WGS project is reported in (e.g., fungi etc.). Our process 
	flow for WGS data provides a data extraction per WGS project with no 
	distinction by molecule (such as mitochondrial). Therefore, some 
	nodes do not include WGS data or may include WGS data for different taxa.
        For instance, NZ_ACSJ01000000 includes contigs representing two tax_ids - 
	a bacterium and a phage.  The entire WGS project has been processed for the 
	complete node and the microbial node in this release.  Therefore, the microbial 
	node includes a small amount of viral sequence and the viral node omits this data. 
    	NZ_ACSJ01000001 to NZ_ACSJ01000011 microbial contigs
    	NZ_ACSJ01000012 to NZ_ACSJ01000019 viral contigs

	[4] Although the goal is to provide a non-redundant collection, some
	redundancy is included in this release as follows:	

	Redundant Protein records:
	    Alternate Splicing		When additional transcripts are provided
					to represent alternate splicing products, 
					and the alternate splice site occurs in 
					the UTR, then the protein is redundantly 
					provided.

	    Paralogs			The goal is to provide a RefSeq record 
					for each naturally occurring molecule. 
					Therefore, records are provided for all 
					genes identified including those produced 
					by more recent gene duplication events in 
					which the genes are nearly identical.
	
	Redundant Genomic records:				
	   Intermediate records		For some species, intermediate genomic 
					records are provided to support the 
					assembly and/or annotation of the genome.
	
					For example, for human, a chromosome may 
					be represented by a chromosome RefSeq 
					record with a NC_ accession prefix.
					The chromosome record may consist of 
					many contigs, each represented as a 
					separate record with a NT_ accession
					prefix. In addition, some curated gene
					region records, with NG_ accession
					prefix, may also be provided to support
					annotation of complex regions.
					
	   Alternate assemblies		Genomic records are provided to represent 
					alternate assemblies of genomic sequence
					derived from different populations. These 
					records will have varying levels of 
					redundancy and represent polymorphic and
					haplotype differences in terms of the
					sequence and annotation.

					For example, alternate assemblies are
					provided for different mouse strains and
					for regions of the human major
					histocompatibility complex (MHC). The MHC
					is a highly variable region of chromosome
					6 which exhibits variation at the level 
					of both sequence polymorphism and gene 
					content. The alternate assemblies make it
					possible to represent this alternate gene
					content. 					

	Microbial strains		Microbial genome sequence data derived from 
		  			different strains may be represented as 
					additional RefSeq records. This introduces 
					redundancy but may also add representation for 
					some proteins that are unique to a strain.  
					RefSeq records for a specific strain can be 
					identified by the unique taxonomic ID for that 
					strain.

	[5] Note that for some organisms, most notably vertebrates, processing to update 
	    individual transcript and protein records may occur on a daily basis. Transcript 
	    and protein updates may include changes to descriptive information such as 
	    publications, names, or feature annotations. Updates can also include changes 
	    to the sequence or the addition of new sequence records. Thus information 
	    available on transcript and protein records may be more current than the 
	    annotated genome.  

2.4 Release Catalog
-------------------
The Release Catalog documents the full contents of the RefSeq Release.
The catalog can be used to identify data of interest.  See the format
description in section 3.5 for additional information.

The release catalog is available at:
  ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/RefSeq-release#.catalog

The catalog for previous releases is available in the archive directory:
  ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/archive/

2.5 Changes since the previous release
--------------------------------------
[1] A list of updated organisms and dbSNP annotation summary is available here: 
    ftp://ftp.ncbi.nih.gov/snp/release-notes/RefSeq/refseq69.snp.rpt 

[2] In this release, we saw almost 50% increase in the count of genomic records in 
the vertebrate_other node, from 2161339 to 3081632. This increase correlates with the 
effort to annotate a large number of bird genome assemblies in late 2014. The complete
list RefSeq genomes annotated by NCBI's Eukaryotic Genome Annotation Pipeline is 
available here: http://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/

Other nodes saw modest increases in record counts.

[3] The International Nucleotide Sequence Database Consortium (INSDC) has introduced a
new feature key 'regulatory' and a set of feature classes. 
http://www.insdc.org/files/feature_table.html#7.2

It is RefSeq's policy to adhere to INSDC formats. NCBI has made the changes necessary 
to start using the new feature key and consequently poly-adenylation signal features are 
now displayed using the new format.

For example:
http://www.ncbi.nlm.nih.gov/nuccore/NM_001303444.1

     regulatory      1191..1196
                     /gene="HEXIM2"
                     /gene_synonym="L3"
                     /regulatory_class="polyA_signal_sequence"


Previous announcements:
-----------------------
[1] A list of updated organisms and dbSNP annotation summary is available here: 
    ftp://ftp.ncbi.nih.gov/snp/release-notes/RefSeq/refseq68.snp.rpt 
[2] New file:
A file named RELEASE_NUMBER has been added to the /refseq/release/ directory. The content
of this file is the integer release number.
[3] Bacterial genomes:
NCBI's refactored Prokaryotic Genome Annotation Pipeline is now in full production mode.
Since the last release, new bacterial genomes from over 8,000 distinct NCBI Taxonomy IDs 
were added to the RefSeq database. This also resulted in a large increase in annotated
bacterial plasmids. 

In addition, approximately 10,000 RefSeq bacterial genomes have been re-annotated and are 
includee in this release.

As bacterial genomes are annotated, they are converted to the new RefSeq protein data model.
Thus, a large number of 'YP_' and 'XP_' accessions have been removed. All pipeline-annotated 
bacterial genomes refer to a nonredundant RefSeq protein with a 'WP_' accession prefix.  We 
will provide a mapping file from the suppressed YP accessions to the replacement WP_ proteins 
when the re-annotation process has completed.  We anticipate this will be available by
December 2014. 

General information on the Prokaryotic Genome Annotation Pipeline is available here:
   http://www.ncbi.nlm.nih.gov/genome/annotation_prok/
   http://www.ncbi.nlm.nih.gov/books/NBK174280/ 

Announcing Future Changes:
--------------------------


=============================================================================
3. ORGANIZATION OF DATA FILES
=============================================================================
3.1 FTP Site Organization
-------------------------
RefSeq releases are available on the NCBI FTP site at:
   ftp://ftp.ncbi.nlm.nih.gov/refseq/release/            

Documentation Directories and Files:
------------------------------------
  release-catalog/
          archive/		   --subdirectory, archive of previous catalogs
	  RefSeq-release#.catalog  --file, comprehensive list of sequence records 
                                     included in the current release
	  release#.files.installed --file, list of sequence data files installed 
	  release#.removed-records --file, list of removed records that were  
                                     included the previous release
          release#.taxon.new       --file, list of organisms that have been
                                     added to the release since the previous release
          release#.taxon.update    --file, list of organisms for which there has
                                     been a change in either the NCBI Tax ID or
                                     the organism name.                                     
  release-notes/
	  archive/		   --subdirectory, archive of previous documentation
	  RefSeq-release#.txt      --file, this Release notes document

  release-statistics/
          archive/                 --subdirectory, archive of previous documentation
         RefSeq-release#.MMDDYYYY.stats.txt --file, release statistics
                                 
Sequence Data Directories and Files:
------------------------------------
The RefSeq collection is provided in a redundant fashion to best meet the needs
of those who want the full collection as well as those who want a specific
sub-set of the collection.  Therefore the collection is provided as: 
   1) the complete collection, and
   2) sections as defined by major taxonomic or other logical groupings. 

A subdirectory exists for each sub-section as follows:
   archaea
   bacteria
   fungi						
   invertebrate	
   mitochondrion	
   plant
   plasmid		
   plastid		
   protozoa	
   vertebrate_mammalian	
   vertebrate_other	
   viral			

In addition, the complete collection is available without these
sub-groupings in the subdirectory:
   complete

Note that this directory structure intentionally provides the release 
data in a redundant fashion. We gave considerable thought to how to
package the release to meet the needs of different user groups. 
For instance, some groups may be interested in retrieving the complete
protein set, while other groups may be interested in retrieving data 
for a more limited number of organisms.  We decided to provide
logical groupings based on general taxonomic node (viral, mammalian etc.)
as well as logical molecule type compartmentalization (e.g., plastid).
Thus, all records are provided at least twice, once in the "complete" 
directory, and a second time in one of the other directories. 
Some sequences may be provided three times when it is logical to 
include the record in more than one additional directory. For example, 
a sequence may be provided in the "complete", "mitochondrion", and 
"vertebrate_mammalian" directories.

We are interested in hearing if you find this structure useful or if
you would like information grouped in a different manner.

Send suggestions or comments to the NCBI Help Desk at:
	info@ncbi.nlm.nih.gov

3.2 Release Contents
--------------------
A comprehensive list of sequence files provided for the current release
is available in:
   ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/release#.files.installed

A comprehensive list of sequence records included in the current release is 
available in:
   ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/release#.catalog

File name format indicates the directory node, molecule type, and format type. 

Name format:

 complete10.bna.gz
|-------|--|---|--|
   1     2   3  4

   1. directory location 
   2. numerical increment (to provide a set of unique file names)
   3. format type 
   4. compression

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, they are all derived from the same initial ASN.1 file.
For example:

   complete1.bna.gz          ---this file represents all of the content found 
                                in the following files.
   complete1.genomic.fna.gz
   complete1.protein.faa.gz
   complete1.rna.fna.gz
   complete1.genomic.gbff.gz
   complete1.protein.gbff.gz
   complete1.rna.gbff.gz

Note that for some molecule and format types, a number increment is skipped.
This is not an error. It is also not an error if a filename provided with one
release is not provided with a different release.  
For example:

   complete103.genomic.gbff
   complete104.genomic.gbff
   complete107.genomic.gbff  --release 38 did not include files named as
                               complete105.genomic or complete106.genomic
                               because complete105.bna & complete106.bna 
                               did not include genomic data.

The RefSeq release processing first produces a comprehensive set of ASN.1 files, 
ordered by tax_id, and limited by a size constraint.  These initial files
are further processed to export the records by molecule and format type.
If the initial ASN.1 file does not include any records for a given molecule type, 
such as genomic sequence data, then the corresponding 'genomic' fasta and 
flatfile records will not be found.

The installed release includes a comprehensive report of all files installed
for a given release. Please refer to /release-catalog/release#.files.installed
(where # is the release number).

3.3 File Names and Formats 
--------------------------
File names are informative, and indicate the content, molecule type,
and file format of each RefSeq release data file. Most filenames
utilize this structure:

	directoryfilenumber.molecule.format.gz
	1        2	    3        4	  

File Name Key:

	1. directory		directory level the file is provided in 
				(e.g.,complete, viral etc)

	2. file	number:		large data sets are provided as incrementally 
				numbered files 

	3. molecule		type of molecule (genomic, rna, or protein); 
				not relevant for ASN.1 format files provided 
				in the "complete" sub-directory

	4. format		the data format provided in the file; see below

For example:
	complete1.genomic.bna.gz
        vertebrate_mammalian2.protein.gpff.gz

RefSeq Whole Genome Shotgun (WGS) data are provided in files provided 
per WGS project.  Their filenames use a slightly different structure:
	directoryWGSproject.molecule.format.gz

For example:
	completeNZ_AAAU.bna.gz
        microbialNZ_AAAV.genomic.fna.gz

All RefSeq release files have been compressed with the gzip utility;
therefore, an invariant ".gz" suffix is present for all release files.

The data that comprises a RefSeq release are available in several
file formats, as indicated by the format component in the file name:
  bna	binary ASN.1 format; includes nucleotide and protein 
  gbff	GenBank flat file format; nucleotide records
  gpff	GenPept flat file format; protein records
  fna	FASTA format; nucleotide records
  faa	FASTA format; protein records

The comprehensive full release is deposited in the "complete"
directory and is available in all file types.

Binary ASN.1 format is only provided in the complete directory. The remaining
directories include all of the remaining file types.

The DDBJ/EMBL/GenBank and GenPept flat file format provided in this release 
matches that seen when accessing the records using the NCBI web site. 
Notably, some RefSeq record are in the CON division and do not instantiate 
the sequence on the flat file display, instead a 'join' statement is provided 
to indicate the assembly instructions.  The FASTA files do include the 
assembled sequences for these CON division RefSeq records.  

For example, see NC_000022.

Suggestions regarding the structure of the RefSeq release product 
and the available formats may be sent to the NCBI Help Desk:
    info@ncbi.nlm.nih.gov

3.4 File Sizes
--------------
RefSeq release files are provided in a range of sizes. Most are
limited to several hundred megabytes (MB) and uncompressed ASN.1 file
size will not exceed 500 MB. Nucleotide FASTA files are split when 
whey reach 1 gigabyte (GB).

Files are compressed to reduce file size and facilitate FTP retrieval.
iebdev21:/panfs/pan1.be-md.ncbi.nlm.nih.gov/rsrelease/release/workdir>more release64.filesize 

The total size of release 69 is as follows:

         Extension    Size (GB)          Type
         -----------------------------------------------------------
         bna          517.93              ASN.1
         gbff         722.49              GenBank flat file
         gpff         288.39              GenPept flat file
         fna          1210.17             FASTA, nucleotide
         faa          47.68               FASTA, protein

Notes: 
 [A] The compete directory provides all file types. The ASN.1 format is only 
     available in the complete directory; the file sizes reported for the 
     remaining file formats represents the redundant total found in the complete 
     plus other directories.

3.5 Statistics
---------------
RefSeq release 69 includes sequences from 51661 different organisms.

The number of species represented in each Release sub-directory, 
determined by counting distinct tax IDs, is as follows: 

        archaea                 860
        bacteria                37639
        complete                51661
        fungi                   2916
        invertebrate            1560
        mitochondrion           5200
        plant                   677
        plasmid                 1927
        plastid                 677
        protozoa                241
        vertebrate_mammalian    728
        vertebrate_other        2534
        viral                   4504

Counts of accessions and basepairs/residues per molecule type:
                 Accessions      Basepairs/Residues 
  Genomic:       11852380        574044044515 
  RNA:           9973568         20408631127 
  Protein:       52276468        18690872100 
  Wgs master:    24603           0 
 

Complete RefSeq release statistics for each directory are provided 
in a separate document. Please see:

   ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-statistics/
   
   file: RefSeq-release#.MMDDYYYY.stats.txt
         #: indicates release number
         MMDDYY: indicates release date as month,day,year
 
Statistics for previous releases are available in the archive subdirectory:
   ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-statistics/archive/

3.6 Release Catalog Format
--------------------------
The full non-redundant contents of the release are documented in the 
release catalog. 

Available at:
   ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/

The catalog includes the following columns:
  1. tax_id
  2. Taxon name
  3. RefSeq accession.version
  4. gi
  5. FTP directories data is provided in, '|' separated
  6. RefSeq status code
  7. sequence length

Note: the molecule type for each catalog entry can be inferred from 
the accession prefix (see below).

RefSeq Status Codes are documented on the RefSeq web site. The catalog includes 
the following terms:

  na			Not Applicable; 
			status codes are not provided for some genomic records

  UNKNOWN		The status code has not yet been applied or status is not
  			applicable to the type of record. 

  REVIEWED		The RefSeq record has been the reviewed by NCBI  
			staff or by a collaborator. Some RefSeq records 
			may incorporate expanded sequence and annotation 
			information including additional publications 
			and features. This indicates a curated record.

  VALIDATED		The RefSeq record has undergone an initial review 
			to provide the preferred sequence standard. The  
			record has not yet been subject to final review 
			at which time additional functional information 
			may be provided. This indicates a curated record.	
			
  PROVISIONAL		The RefSeq record has not yet been subject to 
			individual review and is thought to be well 
			supported and to represent a valid transcript 
			and protein. This record is not curated.
			
  PREDICTED		The RefSeq transcript may represent an ab initio 
			prediction or may be weakly supported by transcripts
			or protein homology. This record is not curated.
			
  INFERRED		The RefSeq record is inferred by genome sequence 
			analysis. This record is not curated.

  MODEL			RefSeq records provided via automated processing 
  			and are not subject to individual review or revision 
			between builds. This record is not curated.

3.7 Removed Records
-------------------
This is a report of accessions that were included in the
previous release but are no longer included in the current release.

Available at:
   ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/
   release#.removed-records file format

The file includes the following columns:

  1. tax_id
  2. species name
  3. RefSeq accession.version
  4. gi
  5. FTP directories data was provided in, in last release
  6. RefSeq status code
  7. sequence length
  8. type of removal
	type options include:
	   dead protein
	   replaced by accession  [original accession is not secondary]
           permanently suppressed
           temporarily suppressed [record may become available again in the future]


3.8 RefSeq Accession Format
---------------------------

RefSeq accessions are formatted as a two letter prefix, followed by 
an underscore, followed by six or nine digits or 4 letters plus eight digits. 
For example, NM_020236, NP_001107345, and NZ_AABC02000001.  

The underscore ("_") is the  primary distinguishing feature of a RefSeq 
accession; DDBJ/EMBL/GenBank accessions never include an underscore.

The RefSeq accession prefix indicates the molecule type. 

  Molecule Type		Accession Prefix
  ----------------------------------------------
  protein		*P_ including: NP_; XP_; AP_; YP_; WP_
  rna			*R_ and *M_ including: NM_; NR_; XM_; XR_
  genomic		NC_; NG_; NT_; NW_; NZ_; NS_; AC_
        
Additional information is available on the RefSeq Web site:

  http://www.ncbi.nlm.nih.gov/RefSeq/key.html#accessions

Transcript and protein accessions are followed by either 6-digits or 9-digits.
For example:
   NP_123456 -or- NP_123456789

As other accession series need to be expanded, they will also be
expanded by adding 3 digits with existing accessions remaining stable.


3.9 Growth of RefSeq
--------------------
Release	Date		Taxons	Nucleotides	Amino Acids	Records
1	Jun 30, 2003	2005	4672871949	263588685	1061675
2	Oct 21, 2003	2124	7745398573	286957682	1097404
3	Jan 13, 2004    2218	7992741222	294647847	1101244
4	Mar 24, 2004    2358	8175128887	318253841	1193457
5	May  3, 2004    2395    8325515623	337229387	1255613
6	July 5, 2004	2467	8696371716	365446682	1367206 
7       Sep 10, 2004    2558	21072808460	405233619	1579579
8       Oct 31, 2004    2645	26814386658	430300369	1709723 
9	Jan  9, 2005    2780	36786975473	470534907	1843944
10	Mar  6, 2005    2827    36893741150     482862858       1893478 
11	May  8, 2005    2928    39731702362     507980644       2477893
12      Jul 10,2005	2969    43043256058     608493108       2869675
13	Sep 11, 2005    3060    44727484853     686768902       3400773
14	Nov 20, 2005    3198	47364955367	763761075	3272776
15      Jan 1, 2006     3244    52645441913     810009733       3436263
16      Mar 11, 2006    3397    56175443059     887509001       3715260 
17	May 1, 2006	3497	62130037371	927587669	3999859 
18      July 11, 2006   3695	70474041999	974374765	4186692
19	Sep 10, 2006    3774    70694879544    1012985077       4311543 
20	Nov 5, 2006	3919	72679681505    1061797276	4567569 
21	Jan 6, 2007	4079	73864990566    1144795927	4742335
22	Mar 5, 2007	4187	82441128546    1215085694	5207865
23	May 8, 2007	4300	83148327110    1291050995	5503385
24	July 10, 2007	4511	89856995521    1365916222	6073814
25	Sep 11, 2007	4646	91265840843    1470475398	6515132 
26	Nov 4, 2007	4737	99105705485    1495032507 	6698250 
27	Jan 6, 2008	4926    101059552113   1556356987	7025715
28	Mar 9, 2008	5059	102051350525   1770627427	7914560
29	May 4, 2008	5168	104671101150   1870214220	8376141
30	July 7,2008	5395	105074486709   1913447691	8572852 
31	Aug 30, 2008	5513	109214348591   2026768719	9145702 
32	Nov 10, 2008	5726	111122203221   2089596746	9501764
33	Jan 16, 2009	7773	116001583818   2204073443      10325282
34	Mar 6, 2009	8054	111792574830   2299682138      10021870
35	May 4, 2009	8393	113210655336   2565199170      10993891
36	July 2, 2009	8665	117013741530   2756884219      12141825
37	Sept 3, 2009    9005	119151229820   2965450333      12941750
38	Nov 7, 2009     9166	119196622435   3115246540      13436447
39	Jan 23, 2010    10171	118502856500   3221054793      13656433
40	Mar 7, 2010 	10291	118645985035   3280528951      13853798
41	May 9, 2010	10567	125500880884   3427514220      14472060
42	July 13, 2010	10728	143311839055   3553178673      15038858
43	Sep 5, 2010	10854	148706971456   3761205880      15934055
44	Nov 7, 2010	11354	152241490865   3899827321      16421261
45      Jan 7, 2011     11536	152787094873   3989526325      16748646
46	Mar 8, 2011	11734	153220856222   4064052954      16998463
47	May 7, 2011	12000	162001966044   4226432170      17631876
48	July 10, 2011	12235	163771272903   4381572480      18162534
49	Sep 7, 2011	16248	162286146420   4401462131      18236994
50 	Nov 8, 2011	16392	168702162406   4529303978      18815153
51	Jan 9, 2012	16609	172751347778   4727472575      19580946
52	Mar 5, 2012	16923	173705194347   4929467422      20235247
53	May 7, 2012	17339	175345433862   5247723883      21286080
54	July 9, 2012	17605	176492228688   5456992181      21889466
55	Sep 17, 2012	17994	194971374545   5803694332      23207572
56	Nov 8, 2012	18512	207200464965   6003283860      23892460
57	Jan 8, 2013	21415	227639108990   8895153979      34158511
58	Mar 11,2013 	22460	233247214400   9699076220      36938203
59	Apr 29, 2013	24656	256547643663   10081118607     39040745
60 	Jul 19, 2013	28560	304686151670   10968281809     40913699
61	Sep 9, 2013	29414	319551394177   11248966865     41958567
62	Nov 10, 2013	31646	361097812819   12364402476     45971929
63  	Jan 12, 2014	33485	380736496721   12898823816     48358066 
64	Mar 10, 2014	33693	407131829420   13126329523     49538213
65	May 12, 2014 	36335	430613954268   13544443640     51770174
66	July 7, 2014	41263	464958653006   15380643722     58334707 
67	Sep 8, 2014 	41913	490800792583   15984799771     61277203 
68	Nov 3, 2014	49312	551290496427   16790850066     66078114
69	Jan 2, 2015 	51661	594452675642   18690872100     74127019

Note: Date refers to the data cut-off date.

=============================================================================
4. FLAT FILE ANNOTATION
=============================================================================

4.1 Main features of RefSeq Flat File
-------------------------------------

Also see the  RefSeq web site and the NCBI Handbook, RefSeq chapter.

   http://www.ncbi.nlm.nih.gov/refseq/
   http://www.ncbi.nlm.nih.gov/books/NBK21091/

4.1.1 LOCUS, DEFLINE, ACCESSION, KEYWORDS, SOURCE, ORGANISM 
--------------------------------------------------------------------
The beginning of each RefSeq records provides information about the accession,
length, molecule type, division, and last update date. This is followed by the 
descriptive DEFINITION line, then by the Accession, version,and GI data, 
followed by detailed information about the organism and taxomonic lineage.

//
LOCUS       NC_004916             384502 bp    DNA     linear   INV 05-JUN-2012
DEFINITION  Leishmania major strain Friedlin complete genome, chromosome 3.
ACCESSION   NC_004916
VERSION     NC_004916.2  GI:389592668
DBLINK      Project: 15564
            BioProject: PRJNA15564
KEYWORDS    RefSeq; complete genome.
SOURCE      Leishmania major strain Friedlin
  ORGANISM  Leishmania major strain Friedlin
            Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae;
            Leishmaniinae; Leishmania.
//

Note: Both the GI and VERSION number increment when a sequence is updated, 
while the ACCESSION remains the same.  The GI and "ACCESSION.VERSION" 
identifiers provide the finest resolution reference to a sequence.

4.1.2 REFERENCE, DIRECT SUBMISSION, COMMENT
-------------------------------------------
REFERENCE: 
While the majority of RefSeq records do include REFERENCE
data, this data is not required and some records do not include any
citations. Publications are propagated from the GenBank record(s) from which
the RefSeq is derived, provided by collaborating groups and NCBI staff
during the curation process, and provided by the National Library of
Medicine (NLM) PubMed MeSH indexing staff as they add new articles to PubMed.

Functionally relevant citations are added by individual scientists using
the Entrez Gene GeneRIF submission form, and a significant volume of citation
connections are supplied by the NLM MeSH indexing staff for human, 
mouse, rat, zebrafish,and cow. This functionality is expected to increase 
in the future to treat all organisms represented in the RefSeq collection.  
Citations supplied by the MeSH indexers and individual scientists can be 
identified by the presence of a REMARK beginning with the text string "GeneRIF".
This represents a significant method to keep sequence connections to the
literature up-to-date; GeneRIFs add considerable value to the RefSeq 
collection.

For more information on GeneRIFs please see:

   http://www.ncbi.nlm.nih.gov/gene/about-generif 

For example, several GeneRIFs have been added to NM_000173.1 including:

// 
REFERENCE   13 (bases 1 to 2480)
  AUTHORS   Poujol,C., Ware,J., Nieswandt,B., Nurden,A.T. and Nurden,P.
  TITLE     Absence of GPIbalpha is responsible for aberrant membrane
            development during megakaryocyte maturation: ultrastructural study
            using a transgenic model
  JOURNAL   Exp. Hematol. 30 (4), 352-360 (2002)
  MEDLINE   21935100
   PUBMED   11937271
  REMARK    GeneRIF: Absence of GPIbalpha is responsible for aberrant membrane
            development during megakaryocyte maturation; leads to abnormal
            partitioning of the membrane systems and abnormal proplatelet
            production.
//

DIRECT SUBMISSION: 
A Direct Submission field is provided on some RefSeq records but not all. It
is propagated from the underlying GenBank record from which the RefSeq is 
derived or provided on submissions from collaborating groups. Transcript
and protein RefSeqs for human, mouse, rat, zebrafish, and cow do not provide
this field as records often include additional data and are not necessarily
direct copies of the GenBank submission.

COMMENT: 
A COMMENT identifying the RefSeq Status is provided for the majority of the 
RefSeq records. This comment may include information about the RefSeq status, 
collaborating groups, and the GenBank records(s) from which the RefSeq is 
derived. The RefSeq COMMENT is not provided comprehensively in this release. 
We are working to supply this COMMENT more comprehensively in the future.

Additional COMMENTS are provided for some records to provide information 
about the sequence function, notes about the aspects of curation, or 
comments describing transcript variants.

A COMMENT is always provided if the GI has changed.
 
For example (from NM_133490):

//
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BC008969.1.
            On Dec 31, 2002 this sequence version replaced gi:19424123.
            
            Summary: Voltage-gated potassium (Kv) channels represent the most
            complex class of voltage-gated ion channels from both functional
            and structural standpoints. Their diverse functions include
            regulating neurotransmitter release, heart rate, insulin secretion,
            neuronal excitability, epithelial electrolyte transport, smooth
            muscle contraction, and cell volume. This gene encodes a member of
            the potassium channel, voltage-gated, subfamily G. This member
            functions as a modulatory subunit. The gene has strong expression
            in brain. Alternative splicing results in two transcript variants
            encoding distinct isoforms.
            
            Transcript Variant: This variant (2) has an alternate 3' sequence,
            as compared to variant 1. It encodes isoform 2 that is shorter and
            has a distinct C-terminus as compared to isoform 1.
//

4.1.3 NUCLEOTIDE FEATURE ANNOTATION
-----------------------------------
Gene, mRNA, CDS:
Every effort is made to consistently provide the Gene and coding sequence (CDS)
feature (when relevant).  If a RefSeq is based on a GenBank record that is only 
annotated with the CDS, then a Gene feature is created.  mRNA features are 
provided for most eukaryotic records; this is not yet comprehensively provided
and will improve in future releases.

Gene Names: 
Gene symbols and names are provided by external official 
nomenclature groups for some organisms.  If official nomenclature is 
not available we may use a systemic name provided by the data submittor 
or apply a more functional name during curation. When official nomenclature 
is available we may provide additional alternate names for some organisms.

Variation:
Variation is computed by the dbSNP database staff and added via post-processing
to RefSeq records.

Miscellaneous:
For some records, additional annotation may be provided when identified by the 
curation staff or provided by a collaborating group. For example, the location 
of polyA signal and sites may be included.

4.1.4 PROTEIN FEATURE ANNOTATION
--------------------------------
Protein Names: 
Protein names may be provided by a collaborating group, may be based on the 
Gene Name, or for some records, the curation process may identify the 
preferred protein name based on that associated with a specific EC number 
or based on the literature.

Protein Products:
Signal peptide and mature peptide annotation is provided by propagation from 
the GenBank submission that the RefSeq is based on, when provided by a 
collaborating group, or when determined by the curation process.

Domains:
Domains are computed by alignment to the NCBI Conserved Domain Database 
database for  human, mouse, rat, zebrafish, nematode, and cow.  The best 
hits are annotated on the RefSeq. For some records, additional functionally 
significant regions of the protein may be annotated by the curation staff.
Domain annotation is not provided comprehensively at this time.

4.2 Tracking Identifiers
------------------------
Several identifiers are provided on RefSeq records that can be used to track 
relationships between annotated features, relationships between RefSeq records, 
and changes to RefSeq records over time. 

The GeneID identifies the related Gene, mRNA, and CDS features. 
Transcript IDs (RefSeq accessions) provide an explicit connection between a 
transcript feature annotated on a genomic RefSeq record, and the RefSeq 
transcript record itself. Likewise, the Protein ID (RefSeq accessions) provides 
the association between the annotated CDS feature on a genomic or transcript 
RefSeq record, and the protein record itself.

Changes to a RefSeq sequence over time can be identified by changes to the GI 
and version number.
	
4.2.1 GeneID
------------
A gene feature database cross-reference qualifier (dbxref), the GeneID, 
is provided on many RefSeq records to support access to the Entrez Gene
database. 

Entrez Gene provides gene-oriented information for a sub-set of the
RefSeq collection. Gene includes data for all Eukaryotic genomes, viral genomes,
and a representative Prokaryotic genomes. 

The GeneID  provides a distinct tracking identifier for a gene
or locus and is provided on the gene, mRNA, and CDS features. The GeneID 
can be used to identify a set of related features; this is especially useful 
when multiple products are provided to represent alternate splicing events.
	
For example:
//
     gene            19683..104490
                     /gene="DLEC1"
		     /db_xref="GeneID:9940"  <<<--- GeneID
                     /db_xref="MIM:604050"
//
	

When viewing RefSeq records via the internet, the GeneID is hot-linked to Entrez
Gene. 

4.2.2 Transcript ID
-------------------
The transcript_id qualifier found on a mRNA or other RNA feature annotation
provides an explicit correspondence between a feature annotation on a genomic 
record and the RefSeq transcript record.

For example:

NT_011523.9      Homo sapiens chromosome 22 genomic contig.
//
     mRNA            complement(231444..239103)
                     /gene="PKDREJ"
                     /product="polycystic kidney disease (polycystin) and REJ
                     (sperm receptor for egg jelly homolog, sea urchin)-like"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq,BLAST. Supporting
                     evidence includes similarity to: 3 mRNAs"
                     /transcript_id="NM_006071.1  <<<--- linked RefSeq transcript
                     /db_xref="GI:5174632"
		     /db_xref="GeneID:10343"
                     /db_xref="MIM:604670"
//

		
4.2.3 Protein ID
----------------
The protein_id qualifier found on a coding region (CDS) feature provides an 
explicit correspondance between feature annotation on a genomic or transcript 
RefSeq record and the RefSeq transcript record.

For example:
NC_001144.4      Saccharomyces cerevisiae chromosome XII, complete sequence.
//      

     CDS             complement(16639..17613)
                     /gene="MHT1"
                     /locus_tag="YLL062C"
                     /experiment="experimental evidence, no additional details
                     recorded"
                     /note="S-methylmethionine-homocysteine methyltransferase,
                     functions along with Sam4p in the conversion of
                     S-adenosylmethionine (AdoMet) to methionine to control the
                     methionine/AdoMet ratio"
                     /codon_start=1
                     /product="Mht1p"
                     /protein_id="NP_013038.1"	<<<--- linked RefSeq protein
                     /db_xref="GI:6322966"
                     /db_xref="SGD:S000003985"
                     /db_xref="GeneID:850664"
 
//

4.2.4 Conserved Domain Database (CDD) ID
----------------------------------------
Protein domain annotation is calculated by the Conserved Domain Database
and is included in RefSeq protein records processed for the FTP site. Domain
annotation appears as a Region feature on protein records and is propagated to
associated transcript features (if available) as a misc_feat. The feature
annotation includes a dbxref cross-reference to the CDD database that is the 
equivalent of a gi identifier in that it may change over time.  The dbxref 
retrieves a domain model as calculated at a point in time; recalculation 
of domains by the CDD group may result in a new CDD identifier value.  The 
CDD dbxref values that are available in the RefSeq release, although not 
stable, will continue to retrieve data from the CDD database where a newer 
identifier value may be found.

For example:
VERSION     NP_000550.2  GI:28302131
DEFINITION  A-gamma globin [Homo sapiens].	     

//
    Region          5..142
                     /region_name="globin"
                     /note="Globins are heme proteins, which bind and transport
                     oxygen; cd01040"
                     /db_xref="CDD:29979"  <<--- CDD identifier
//

=============================================================================
5. REFSEQ ADMINISTRATION
=============================================================================
The National Center for Biotechnology Information (NCBI), National Library
of Medicine, National Institutes of Health, is responsible for the production
and distribution of the NIH RefSeq Sequence Database. NCBI distributes
RefSeq sequence data by anonymous FTP. For more information, you may contact 
NCBI by email at info@ncbi.nlm.nih.gov or by phone at 301-496-2475.

5.1 Citing RefSeq
-----------------
When citing data in RefSeq, it is appropriate to to give the sequence name,
and primary accession and version number (or GI). Note, the most accurate
citation of the sequence is provided by including the combined accession plus
version number or the GI number.

It is also appropriate to list a reference for the RefSeq project. Please
refer to the RefSeq web site for the most recent publication.
  http://www.ncbi.nlm.nih.gov/refseq/publications/

5.2 RefSeq Distribution Formats
-------------------------------
Complete flat file releases of the RefSeq database are available via
NCBI's anonymous ftp server:
	ftp://ftp.ncbi.nlm.nih.gov/refseq/release/

Each release is cumulative, incorporating previous data plus new data.
Records that have been suppressed are not included in the release.

Incremental updates that become available between RefSeq releases
are available at:

ftp://ftp.ncbi.nlm.nih.gov/refseq/daily
ftp://ftp.ncbi.nlm.nih.gov/refseq/cumulative

Please refer to the README for additional information:
ftp://ftp.ncbi.nlm.nih.gov/refseq/README



5.3 Other Methods of Accessing RefSeq Data
------------------------------------------

Entrez is a molecular biology database system that presents an integrated
view of DNA and protein sequence data, structure data, genome data, 
publications, and other data fields.  The Entrez query and retrieval
system is produced by the National Center for Biotechnology Information
(NCBI) and is available only via the internet.

Entrez is accessed at:

	http://www.ncbi.nlm.nih.gov/Entrez/

RefSeq entries are indexed for retrieval in the Entrez system. The web-based
filter restrictions can be used to restrict your query to RefSeq data or to 
specific subsets of the RefSeq database.

Additional specific property restrictions are provided to support querying
for RefSeq records with specific STATUS codes. Queries are defined on the
RefSeq web site at:

	http://www.ncbi.nlm.nih.gov/RefSeq/

5.4 Request for Corrections and Comments
----------------------------------------
We welcome your suggestions to improve the RefSeq collection; we invite 
groups interested in contributing toward the collection and curation 
of the RefSeq database to improve the representation of single genes, 
gene families, or complete genomes to contact us.

Please refer to RefSeq accession and version numbers (or GI) and the RefSeq
Release number to which your comments apply; it is useful if you
indicate the source of data that you found to be problematic (e.g., data on
the FTP site, data retrieved on the web site), the entry DEFLINE, and the 
specific annotation field for which you are suggesting a change.

Suggestions and corrections can be sent to:

	info@ncbi.nlm.nih.gov

5.5 Credits and Acknowledgements
--------------------------------
This RefSeq release would not be possible without the support of numerous
collaborators and the primary sequence data that is submitted by thousands
of laboratories and available in GenBank.

The RefSeq project is ambitious in scope and we actively welcome opportunities
to work with other groups to provide this collection. We value all of our 
collaborators; they contribute information with a large range in scope and 
volume such as completely annotated genomes, advice to improve the sequence 
or annotation of individual RefSeq records, information about official 
nomenclature, and information about function.

In addition to the significant information collected by collaboration, 
numerous NCBI staff are involved in infrastructure support, programmatic 
support, and curation. RefSeq is supported by 3 primary work groups that 
are associated with Entrez Gene, Entrez Genomes, and the Genome Annotation 
Pipeline. 

5.6 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.