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README for ftp://ncbi.nlm.nih.gov/refseq/release/release-catalog
Last updated: December 21, 2022
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_________________________________________________________________________
National Center for Biotechnology Information (NCBI)
National Library of Medicine
National Institutes of Health
8600 Rockville Pike
Bethesda, MD 20894, USA
tel: (301) 496-2475
fax: (301) 480-9241
e-mail: info@ncbi.nlm.nih.gov
_________________________________________________________________________
Updates:
December 21, 2022
Changed CRC checksum to MD5 checksum
December 4, 2020
The 'release#.files.installed' section was modified to add the names of
the columns, CRC checksum and File name
January 11, 2018
The following sections were updated to reflect dropping of gi numbers,
and other changes.
'RefSeq-release#.catalog' now contain 6 columns instead of 7
- 'gi' deleted as column 4
'release#.removed-records' now contains 7 columns instead of 8
- 'gi' deleted as column 4
'release#.AutonomousProtein2Genomic.gz' now contains 6 columns,
instead of 5
- 'Protein gi' deleted as column 2
- 'Nucleotide gi' deleted as column 4
- 'Strain-level tax_id' added as column 3
- 'BioSample' added as column 5
- 'Species name' added as column 6
'release#.MultispeciesAutonomousProtein2taxname.gz' now contains
3 columns instead of 4
- 'Protein gi' deleted as column 2
July 21, 2017
The 'release#.files.installed' section was modified to clarify the
relationship between files with the same numerical increment.
October 21, 2016
Updated two file names to match the file names in
ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/
release#.WP2genomic.mapping.txt.gz was updated to
release#.AutonomousProtein2Genomic.gz
release#.multispecies_WP_accession_to_taxname.txt.gz was updated to
release#.MultispeciesAutonomousProtein2taxname.gz
November 21, 2013
Added documentation for files:
release#.WP2genomic.mapping.txt.gz
release#.multispecies_WP_accession_to_taxname.txt.gz
November 23, 2005
New file provided with the release:
release#.accession2geneid
March 10, 2005
New files provided with the release:
release#.taxon.new
release#.taxon.update
April 5, 2004
RefSeq-release4.txt was updated to remove redundancy
The original is available as RefSeq-release4.originalwithduplicates.txt
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This directory includes files documenting the contents of the RefSeq release
both as an accession list and file list, and records that were included in the
previous release but are not included in the current release.
Files included are:
RefSeq-release#.catalog
release#.files.installed
release#.removed-records
release#.taxon.new
release#.taxon.update
release#.accession2geneid
release#.WP2genomic.mapping.txt.gz
release#.multispecies_WP_accession_to_taxname.txt.gz
where '#' is the release number
Subdirectories:
archive - previous release catalogs are available here
==========================================
RefSeq-release#.catalog
==========================================
Content: Tab-delimited listing of all accessions included in the current
RefSeq release.
Columns:
1. taxonomy ID
2. species name
3. accession.version
4. refseq release directory accession is included in
complete + other directories
'|' delimited
5. refseq status
na - not available; status codes are not applied to most genomic records
INFERRED
PREDICTED
PROVISIONAL
VALIDATED
REVIEWED
MODEL
UNKNOWN - status code not provided; however usually is provided for
this type of record
6. length
==========================================
release#.files.installed
==========================================
Content: Tab-delimited list of sequence files installed for the current release
and the corresponding MD5 checksum.
Columns:
1. MD5 checksum
2. File name
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
3. format type
4. compression
Multiple files may be provided for any given molecule and format type, indicated
by a numerical increment in the file names. Files of the same molecule type and
increment are related by content. Files of different molecule type and the same
increment may or may not have related content. For example:
complete.1006.bna.gz
complete.1006.1.genomic.fna.gz, complete.1006.2.genomic.fna.gz
-- genomic FASTA split into two sub-parts due to size
complete.1006.genomic.gbff.gz -- content related to the two 1006.#.genomic.fna.gz files
complete.1006.protein.faa.gz, complete.1006.protein.gpff.gz
-- contains proteins found in either genomic or rna files of this increment
complete.1006.rna.fna.gz
complete.1006.rna.gbff.gz -- unrelated to the contents of the genomic files of this increment
If you are interested in a complete set of genomic, protein, and rna files for a given
tax_id, you must scan all files from the directory. You may also want to consider using
the per-assembly files provided at ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/ instead.
More information is available at:
https://www.ncbi.nlm.nih.gov/genome/doc/ftpfaq/
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.
For example:
complete10.bna.gz
complete10.genomic.fna.gz
complete10.genomic.gbff.gz
complete10.protein.faa.gz
complete10.protein.gpff.gz
complete10.rna.fna.gz
complete10.rna.gbff.gz
If complete10.bna.gz includes genomic, and RNA, and protein data then the
full set of files are provided.
In contrast, if complete24.bna includes only genomic and protein data
then the corresponding rna file is not provided:
complete24.bna.gz
complete24.genomic.fna.gz
complete24.genomic.gbff.gz
complete24.protein.faa.gz
complete24.protein.gpff.gz
==========================================
release#.removed-records
==========================================
Content: Tab-delimited report of records that were included in the previous
release but are not included in the current release.
Columns:
1. taxonomy ID
2. species name
3. accession.version
4. refseq release directory accession is included in
complete + other directories
'|' delimited
5. refseq status
na - not available; status codes are not applied to most genomic records
INFERRED
PREDICTED
PROVISIONAL
VALIDATED
REVIEWED
MODEL
UNKNOWN - status code not provided; however usually is provided for
this type of record
6. length
7. removed status
dead protein: protein was removed when genomic record was reloaded
and protein was not found on the nucleotide update.
This is an implied permanent suppress.
temporarily suppressed: record was temporarily removed and may be
restored at a later date.
permanently suppressed: record was permanently removed. It is possible
to restore this type of record however at the
time of removal that action is not anticipated.
replaced by accession: the accession in column 3 has become a secondary
accession that cited in column 8.
==========================================
release#.taxon.new
==========================================
Content: tab delimited report of organisms that have been added to the RefSeq
collection since the previous release.
Columns:
1. taxonomy ID
2. species name
3. refseq release directory that data is included in
complete + other directories
'|' delimited
==========================================
release#.taxon.update
==========================================
Content: Report of organisms for which either the NCBI taxonomy ID or the
species name has been modified since the previous release.
Columns ('|' delimited):
1. taxonomy ID, current
2. species name, current
3. taxonomy ID, previous
4. species name, previous
==========================================
release#.accession2geneid
==========================================
Content: Report of GeneIDs available at the time of the RefSeq release.
Limited to GeneIDs that are associated with RNA or mRNA records with
accession prefix N[M|R] and X[M|R].
Columns (tab delimited):
1: Taxonomic ID
2: Entrez GeneID
3: Transcript accession.version
4: Protein accession.version
na if no data
--for example, the NR_ accession prefix is used for RNA
so there is no corresponding protein record
==========================================
release#.AutonomousProtein2Genomic.gz
==========================================
Content: Report of genomic accessions that nonredundant WP
protein accessions are annotated on. Multiple rows are provided
for nonredundant proteins that have been annotated on multiple
genomic records.
Columns:
1: Protein accession.version
2: Genomic nucleotide accession.version
3. Strain-level tax_id
4: Species-level tax_id
5: BioSample
6: Species name
=====================================================
release#.MultispeciesAutonomousProtein2taxname.gz
=====================================================
Content: Report of the NCBI TaxID and species names for the subset
of nonredundant proteins (WP accession) which are annotated on genomic
records from more than one species.
Columns:
1: Protein accession.version
2: Species-level tax_id of genomic record(s) that the protein is annotated on
3: Species name (string)