******************************************************************************

RefSeq-release12.txt       ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/

		NCBI Reference Sequence (RefSeq) Database

			Release 12
			July 10, 2005

		Distribution Release Notes
Release Size: 
2969 organisms, 43043256058 nucleotide bases, 608493108 amino acids, 2869675 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 Handbook:  
   http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=handbook.TOC&depth=2
 
2. RefSeq Web Site: 
   http://www.ncbi.nlm.nih.gov/RefSeq/

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 12
	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 Last genome update for select major organisms
	2.5 Release Catalog
	2.6 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 and LocusID
		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.

1.1 Release 12
-------------

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 in-house staff comprised of expert 
biologists.  

RefSeq release 12 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 12, incorporates data available as of July 10, 2005. 
For more recent data, users are advised to:
	
	. Download the RefSeq daily update files from the RefSeq FTP site
	     ftp://ftp.ncbi.nih.gov/refseq/daily

	
	. Use the interactive web Entrez Query systems to query based on 
	  date
             http://www.ncbi.nlm.nih.gov/Entrez/




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.  For genomes
included in the LocusLink database, validation ensures consistency
is maintained for descriptive information (symbols, gene and protein names)
between RefSeq and LocusLink 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. 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 release includes records representing 2969 distinct taxonomic categories,
as measured by counting the number of distinct tax_ids included in the release.
Tax_ids are provided, for all species having any amount of sequence data, by the 
NCBI Taxonomy group. 

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 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, 
as is the case with Danio rerio (zebrafish).


2.3 Known Problems, Redundancies, 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 Danio rerio (zebrafish), Bos taurus (cow), and Leishmania 
	major. As additional sequence data becomes available, the RefSeq 
	representation for these, and other, organisms will increase. 
	
	[3] 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 occuring 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		We are evaluating how to best represent 
					microbial genome sequence data derived from
					different strains in the RefSeq collection.
					At this time, sequence 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.  We are planning to introduce a new
					identifier, a 'project ID', in the near future. 
					The project ID will facilitate identification of
					this known redundancy.


   
2.4 Notes on select major organisms
-----------------------------------

Anopheles gambiae		Genomic sequence data is available as 
				whole genome shotgun (WGS). This release includes  
                                an annotation update released by Ensembl 
                                (Ensembl release 31.2f; NCBI build 2.2).

Apis mellifera			The assembled genome was provided by Baylor College
                                of Medicine. This release includes the NCBI annotation
                                build 2.1. 

Arabidopsis thaliana		An annotation update, release 5.0, was provided by
				TIGR in February, 2004. The RefSeq release includes 
				chromosomes, transcripts, and proteins. 

Bos taurus			A 3X WGS assembly was released in October, 2004 by 
                                Baylor College of Medicine. The initial assembly
                                provides contigs with no chromosome placement.
                                This RefSeq release includes the NCBI annotation of 
				this initial WGS assembly.

Canis familiaris		A 7.8X dog genome WGS assembly was release in July 2004
				by the Dog Genome Sequencing Consortium. The assembly
				was annotated by the NCBI genome annotation pipeline
				(NCBI build 1.1) and is included in this RefSeq release.
                                
Caenorhabditis elegans		The RefSeq release includes an annotation update 
				that was released on October 16, 2003 the genome
                                version available on March 7, 2003 (genome release 2.0). 
				The release includes chromosome, transcript, and 
				protein records. An update is anticipated for the next
                                RefSeq release.

Danio rerio			This RefSeq release includes the genome assembly Zv4
                                provided by the Zebrafish Genome Project and the 
                                NCBI annotation of this assembly.

Drosophila melanogaster		Updated - Release 4.1 of the assembled, annotated genome 
				was provided by FlyBase in March 2005
                               
Encephalitozoon cuniculi        The annotated assembled genome was contributed by
                                Genoscope and the Universite Blasie Pascal.

Eremothecium gossypii		The annotated assembled genome was contributed by
                                the University of Basel in collaboration with Syngenta.
				  
Gallus gallus			The assembled genome was provided by the Washington
                                University School of Medicine. This release includes
                                the NCBI Map Viewer annotation build 1.1 (released
                                July 2004).
                                                                 
Homo sapiens			NCBI provides the human genome assembly in close
				collaboration with the sequencing centers. 
				This release includes human genome build 35.1.
                                A new assembly and annotation build is planned and
                                may be available in one of the next 2 RefSeq releases.
			       
				The release includes RefSeq chromosomes, contigs, 
				known transcripts and proteins (as defined by 
				having a Gene ID), and derived model transcripts 
				and proteins predicted by the Genome Annotation 
				pipeline. See: 
				http://www.ncbi.nlm.nih.gov/genome/guide/build.html

Magnaporthe grisea		The assembled annotated WGS genome was provided by the 
				Whitehead Institute and RefSeqs were available on 
				December 29, 2003. The release includes genomic,
				transcript, and protein records.
 
Mus musculus			NCBI provides the mouse genome assembly in close
				collaboration with the sequencing centers. 
				This RefSeq release includes mouse genome build 34.1. 
                                An updated assembly and annotation build will 
                                be available soon.
				
				The release includes RefSeq contigs, known 
				transcripts and proteins, and derived model 
				transcripts and proteins predicted by the Genome
				Annotation pipeline. 

Neurospora crassa 		The annotated genome data was supplied by the Whitehead
				Institute. RefSeqs were released on July 2, 2003
				and include WGS genomic contigs, predicted transcripts,
				predicted proteins. The RefSeq data does not represent
				the subset of small WGS contigs that were not
				mapped to a chromosome position or do not include 
				annotation.
 
Oryza sativa			The genome is being sequenced by the International
				Rice Genome Sequencing Project. RefSeqs are provided 
				by NCBI processing to generate the annotated
				genomic contigs; annotation is propagated from 
				the submitted BAC clones. The RefSeq assembly
                                was generated on October 27, 2004 using
                                annotation propagated from the submitted BACs.

Pan troglodytes			The chimpanzee genome was assembled by the Broad Institute
                                and the Washington University School of Medicine using
                                the human genome as a guide.  The assembly
				was annotated by the NCBI genome annotation pipeline
				(NCBI build 1.1) and is included in this RefSeq release.
  
Rattus norvegicus		Updated - NCBI uses the rat whole genome shotgun (WGS) 
				genome assembly provided by Baylor sequencing 
				center. The RefSeq includes rat genome 
				build 3.1 which is based on the RGSC v3.4 assembly, 
				provided by the Rat Genome Sequencing Consortium 
				(RGSC).  RefSeqs include contigs, known transcripts
				and proteins, and derived model transcripts and
				proteins predicted by the Genome Annotation pipeline.		

Saccharomyces cerevisiae	Updated - Provided by Sacchraomyces Genome Database (SGD);
                                this release includes the chromosome and protein
                                records updated June 27, 2005.
                              

Schizosaccharomyces pombe	Updated - Provided by Sacchraomyces Genome Database (SGD);
                                this release includes the chromosome and protein
                                records updated on June 20, 2005.

Microbial			The RefSeq collection includes incomplete
				WGS microbial genomes for which an accession
				is provided for each contig; thus, the 
				number of accessions for this category is 
				significantly greater than the number of organisms
				represented.

				This RefSeq release includes 236 complete microbial 
				genomes. Microbial genomes are annotated by 
				a collaborative automatic computation method, 
				followed by curation by NCBI staff. 

				Complete microbial genomes that have become available in
				RefSeq since the last release:	
			
				Corynebacterium jeikeium K411   
				Xanthomonas campestris pv. campestris str. 8004 
				Sulfolobus acidocaldarius DSM 639       
			
				 				  
				Nineteen microbial genomes have been curated:
				  Aeropyrum pernix
				  Archaeoglobus fulgidus
				  Buchnera sp. APS
				  Buchnera aphidicola Sg
				  Corynebacterium glutamicum
				  Escherichia coli K-12
                                  Escherichia coli O157:H7
				  Haemophilus influenzae
				  Lactococcus lactis subsp. lactis
				  Mycoplasma genitalium
				  Mycoplasma pneumoniae
				  Oceanobacillus iheyensis
                                  Salmonella typhimurium LT2
				  Shewanella oneidensis
				  Pyrococcus abyssi
				  Pyrococcus furiosus
				  Pyrococcus horikoshii
				  Thermoplasma volcanium
				  Vibrio vulnificus CMCP6 
		

Viruses				This RefSeq release includes over 1500 distinct viral
				genome records which have been curated via an extensive
				collaboration between the international virologist
				community and NCBI staff virologists. A panel of
				viral genomes advisors has been established. 

				

For more information please see:

RefSeq Collaborations:  http://www.ncbi.nlm.nih.gov/RefSeq/collaborators.html
Viral Genome Advisors:  http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/viradvisors.html
Microbial Contributors: http://www.ncbi.nlm.nih.gov/RefSeq/microbialcontrib.html
				

2.5 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.nih.gov/refseq/release/release-catalog/RefSeq-release#.catalog

The catalog for previous releases is available in the archive directory:

  ftp://ftp.ncbi.nih.gov/refseq/release/release-catalog/archive/



2.6 Changes since the previous release
--------------------------------------

There are no major changes in annotation format or 
features annotated with this release. 

Previously Announced Changes:

Announced for RefSeq Release 11:
dbxref annotations:
   HPRD:	A new dbxref is provided for a subset of human records.
                The Human Protein Reference Database (HPRD) is providing
                protein annotation information including binding sites
                and modifications for a subset of the human RefSeq
                dataset. When HPRD has some protein data for a gene,
                the RefSeq Gene feature includes an additional dbxref to
                the HPRD data source (http://www.hprd.org/)


                /db_xref="HPRD:HPRD_00218"


Protein feature annotations:
   HPRD is providing protein feature annotation for protein modification
   sites. HPRD is also providing protein:protein interaction data which 
   is available in Entrez Gene.

   This feature annotation is not displayed on the Entrez Flat File display
   by default; one must check the 'HPRD' check box, located above the sequence
   record display in the gray bar, and refresh the display in order to see
   this annotation.  These features are included in the RefSeq release flat
   file format files.

      Examples:
      NP_009225.1
      Site            1423
                     /site_type="phosphorylation"
                     /citation=[238]
                     /evidence=experimental
                     /db_xref="HPRD:06347"

      NP_006163.1
      Site            123
                     /site_type="modified"
                     /note="proteolytic cleavage site"
                     /citation=[20]
                     /citation=[24]
                     /evidence=experimental
                     /db_xref="HPRD:05573"

Nucleotide STS feature annotation:
   STS features are being calculated by the UniSTS database group for inclusion on
   RefSeq nucleotide records.  Some STS features may be provided redundantly during
   the process of convertion to this new method.  

   This feature annotation is not displayed on the Entrez Flat File display
   by default; one must check the 'STS' check box, located above the sequence
   record display in the gray bar, and refresh the display in order to see
   this annotation.  These features are included in the RefSeq release flat
   file format files.

   Example:
     NM_001089.1
     STS             6319..6474
                     /gene="ABCA3"
                     /standard_name="SHGC-61174"
                     /db_xref="UniSTS:83514"



Announced for RefSeq Release 10:
New files included in the release:
  release#.taxon.new   -- reports new organisms added to the release
                       catalog since the previous release
       
  release#.taxon.update -- reports organisms for which either the
                        NCBI Tax ID value has been modified, or the
                        organism name has changed.

dbxref annotations:
  CCDS:     RefSeq transcript and protein records for human include
            a new dbxref annotation to indicate records that have
            a Consensus Coding Sequence (CCDS) identifier association.
            See the CCDS project web site for additional information:
            http://www.ncbi.nlm.nih.gov/projects/CCDS/
     
  LocusID:  These dbxref annotation are obsolete and have been replaced
            by GeneID dbxref annotations. LocusID dbxrefs are being removed
            over time and therefore some records may still include them in the
            ASN.1 format. 
 

=============================================================================
3. ORGANIZATION OF DATA FILES
=============================================================================

3.1 FTP Site Organization
-------------------------

RefSeq releases are available on the NCBI FTP site at:

   ftp://ftp.ncbi.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:

   fungi						
   invertebrate	
   microbial	
   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.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.nih.gov/refseq/release/release-catalog/release#.catalog

File name format indicates the directory node, molecule type, and 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, they are all derived from the same ASN.1 file.

Name format:

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

   1. directory location 
   2. numerical increment
   3. format type 
   4. compression 

Note that for some molecule and format types, a number increment is skipped.
This is not an error.  The RefSeq release processing first produces a set of 
split ASN.1 files which are used to export the records by molecule and format 
type. If an 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.



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. However, some of the genomic
FASTA files can exceed 2Gb.

Files are compressed to reduce file size and facilitate FTP retrieval.

The total size of release 12 is as follows:

         Extension    Size (GB)          Type
         -----------------------------------------------------------
         bna          13.94               ASN.1
         gbff         19.69               GenBank flat file
         gpff         9.04                GenPept flat file
         fna          86.91               FASTA, nucleotide
         faa          1.40                FASTA, protein


Note: 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 12 includes sequences from 2969 different organisms.

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


	complete              	2969
	fungi                 	57
	invertebrate          	168
	microbial             	620
	mitochondrion         	738
	plant                 	41
	plasmid               	404
	plastid               	43
	protozoa              	51
	vertebrate_mammalian  	146
	vertebrate_other      	347
	viral                 	1504


Total Number of Accessions and Length (number of nucleotides or amino 
acids), per type of molecule:

Counts of accessions and basepairs/residues per molecule type:

	  	 Accessions 	 Basepairs/Residues 
  Genomic:	 677974      	 42219703276 
  RNA:    	 495772      	 823552782 
  Protein:	 1695929     	 608493108 

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

   ftp://ftp.ncbi.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.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.nih.gov/refseq/release/release-catalog/

The catalog includes the following columns:

  1. tax_id
  2. species name
  3. RefSeq accession.version
  4. gi
  5. FTP directories data is provided in
  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 

  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.

  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.	
			
  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.
			
  PREDICTED		The RefSeq transcript may represent an ab initio 
			prediction or may be partially supported by other 
			transcript data; the protein is predicted.
			
  INFERRED		The RefSeq record is inferred by genome sequence 
			analysis.

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

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.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 digits or 4 letters plus eight digits. 
For example, NM_020236 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		NP_; XP_; ZP_; AP_; YP_;
  rna			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


NOTICE OF CHANGE:
NP_ accession space has been expanded to 9 digits.
The new format is NP_123456789. Existing 6-digit accessions remain
unchanged. That is, accessions such as NP_013474 were not
modified to 9 digits.

As other accession series need to be expanded, they will also be
expanded by adding 2 digits with existing accessions remaining stable.


3.9 Growth of RefSeq
--------------------

Release	Date		Species	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

=============================================================================
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/bv.fcgi?call=bv.View..ShowTOC
   &rid=handbook.TOC&depth=2


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             384518 bp    DNA     linear   INV 26-JUN-2003
DEFINITION  Leishmania major chromosome 3, complete sequence.
ACCESSION   NC_004916
VERSION     NC_004916.1  GI:32189699
KEYWORDS    .
SOURCE      Leishmania major
  ORGANISM  Leishmania major
            Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae;
            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 LocusLink 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/LocusLink/GeneRIFhelp.html


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 RefSeq records to support access to the Entrez Gene
database. 

Entrez Gene provides gene-oriented information for the entire
RefSeq collection. 

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 and the LocusID is hot-linked to the LocusLink Gene Report page. Both 
resources provide additional descriptive information for genes, as available. 


4.2.2 Transcript ID
-------------------

The transcript_id qualifier found on a mRNA or other RNA feature annotation
provides an explicit correspondance 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="LocusID: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_001144.2      Saccharomyces cerevisiae chromosome XII, complete chromosome
                 sequence.
//      
 CDS             complement(16639..17613)
                     /gene="MHT1"
                     /locus_tag="YLL062C"
                     /note="Mht1p;
                     go_component: cellular_component unknown [goid 8372]
                     [evidence ND];
                     go_function: homocysteine S-methyltransferase activity
                     [goid 8898] [evidence IDA] [pmid 11013242];
                     go_process: sulfur amino acid metabolism [goid 96]
                     [evidence IMP] [pmid 11013242]"
                     /codon_start=1
                     /evidence=experimental
                     /product="S-Methylmethionine Homocysteine
                     methylTransferase"
                     /protein_id="NP_013038.1"	<<<--- linked RefSeq protein
                     /db_xref="GI:6322966"
                     /db_xref="SGD:S0003985"
		     /db_xref="GeneID:850664"
                     /translation="MKRIPIKELIVEHPGKVLILDGGQGTELENRGININSPVWSAAP
                     FTSESFWEPSSQERKVVEEMYRDFMIAGANILMTITYQANFQSISENTSIKTLAAYKR
                     FLDKIVSFTREFIGEERYLIGSIGPWAAHVSCEYTGDYGPHPENIDYYGFFKPQLENF
                     NQNRDIDLIGFETIPNFHELKAILSWDEDIISKPFYIGLSVDDNSLLRDGTTLEEISV
                     HIKGLGNKINKNLLLMGVNCVSFNQSALILKMLHEHLPGMPLLVYPNSGEIYNPKEKT
                     WHRPTNKLDDWETTVKKFVDNGARIIGGCCRTSPKDIAEIASAVDKYS"
//


4.2.4 Conserved Domain Database (CDD) ID
----------------------------------------

The CDD identifier found on protein records, and mapped to associated 
nucleotide records as a misc_feat,identifies protein domains that are
found on the record. CDD annotation is applied computationally. Initially
this annotation was provided for a subset of RefSeq; it will be applied
to the entire collection in the near future.

For example:

NP_000550.2	     A-gamma globin

//

     Region          5..147
                     /region_name="Globin"
                     /note="globin"
                     /db_xref="CDD:pfam00042"  <<<--- conserved domain database

//


=============================================================================
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. The 
following on-line publication provides the most complete description and
should be cited when possible:

   The NCBI handbook [Internet]. Bethesda (MD): National Library of 
   Medicine (US), National Center for Biotechnology Information; 2002 
   Oct. Chapter 17, The Reference Sequence (RefSeq) Project. 
   Available from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books 

If on-line citations are not accepted by a journal, please use the following
citation:

  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database 
  of genomes, transcripts and proteins 
  Pruitt KD, Tatusova, T, Maglott DR 
  Nucleic Acids Res 2005 Jan 1;33(1):D501-D504
 


5.2 RefSeq Distribution Formats
-------------------------------

Complete flat file releases of the RefSeq database are available via
NCBI's anonymous ftp server:

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

Please refer to the README for additional information:
ftp://ftp.ncbi.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 LocusLink, Entrez Genomes, and the Genome Annotation 
Pipeline. 

See the RefSeq web site for a list of collaborating groups and in-house
staff.


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.