Greetings GenBank Users,
An experimental CON-division file has been included with GenBank releases
since December of 1999. More information about CON-division records can be
found in this README at the NCBI ftp site:
ftp://ftp.ncbi.nih.gov/genbank/README.genbank
and in this NCBI News article:
http://www.ncbi.nlm.nih.gov/Web/Newsltr/Fall99/contig.html
Starting on Wednesday, January 15, a new class of incremental-update product
for CON-division records will be made available, in these directories :
ftp://ftp.ncbi.nih.gov/ncbi-asn1/daily-nc/ftp://ftp.ncbi.nih.gov/genbank/daily-nc/
The files will utilize these naming conventions (respectively) :
con_nc.MMDD.aso.gz (ASN.1)
con_nc.MMDD.flat.gz (GenBank Flatfile)
As described in README.genbank, CON-division records can be generated for:
a) complete genomes that have been split into pieces; and b) 'segmented sets',
utilized for genes/regions that have been incompletely sequenced.
Initially, only complete-genome CON-division records will be present in
the new data products. The submission rate of complete-genomes is
currently relatively low, so there will often be no con_nc* files on any
given day .
A sample CON-division record is enclosed below. CON records have no coding
region annotation and no actual sequence data, so there will be no GenPept,
protein-FASTA, or nucleotide-FASTA versions of the incremental CON-division
data product.
Mark Cavanaugh
GenBank
Sample CON-division flatfile :
LOCUS AE015929 2499279 bp DNA circular CON 02-JAN-2003
DEFINITION Staphylococcus epidermidis ATCC 12228, complete genome.
ACCESSION AE015929
VERSION AE015929.1 GI:27316888
KEYWORDS .
SOURCE Staphylococcus epidermidis ATCC 12228
ORGANISM Staphylococcus epidermidis ATCC 12228
Bacteria; Firmicutes; Bacillales; Staphylococcus.
REFERENCE 1 (bases 1 to 2499279)
AUTHORS Zhang,Y., Ren,S., Li,H., Fu,G., Lu,L., Lu,G., Jia,J., Tu,Y.,
Qin,Z., Chen,Z. and Wen,Y.
TITLE Direct Submission
JOURNAL Submitted (05-NOV-2002) Chinese National Human Genome Center at
Shanghai, 250 Bi Bo Road, Shanghai 201203, China
FEATURES Location/Qualifiers
source 1..2499279
/organism="Staphylococcus epidermidis ATCC 12228"
/strain="ATCC 12228"
/db_xref="ATCC:12228"
/db_xref="taxon:176280"
CONTIG join(AE016744.1:1..300787,AE016745.1:61..300242,
AE016746.1:61..303211,AE016747.1:61..300892,AE016748.1:61..300029,
AE016749.1:61..302823,AE016750.1:61..300698,AE016751.1:61..300275,
AE016752.1:61..90802)
//
Sample CON-division ASN.1 :
Seq-entry ::= seq {
id {
genbank {
accession "AE015929" ,
version 1 } ,
gi 27316888 } ,
descr {
source {
genome genomic ,
org {
taxname "Staphylococcus epidermidis ATCC 12228" ,
db {
{
db "taxon" ,
tag
id 176280 } ,
{
db "ATCC" ,
tag
id 12228 } } ,
orgname {
name
binomial {
genus "Staphylococcus" ,
species "epidermidis" } ,
mod {
{
subtype strain ,
subname "ATCC 12228" } } ,
lineage "Bacteria; Firmicutes; Bacillales; Staphylococcus" ,
gcode 11 ,
div "BCT" } } } ,
pub {
pub {
sub {
authors {
names
std {
{
name
name {
last "Zhang" ,
first "Yueqing" ,
initials "Y." } } ,
{
name
name {
last "Ren" ,
first "Shuangxi" ,
initials "S." } } ,
{
name
name {
last "Li" ,
first "Hualing" ,
initials "H." } } ,
{
name
name {
last "Fu" ,
first "Gang" ,
initials "G." } } ,
{
name
name {
last "Lu" ,
first "Lingfeng" ,
initials "L." } } ,
{
name
name {
last "Lu" ,
first "Gang" ,
initials "G." } } ,
{
name
name {
last "Jia" ,
first "Jia" ,
initials "J." } } ,
{
name
name {
last "Tu" ,
first "Yuefeng" ,
initials "Y." } } ,
{
name
name {
last "Qin" ,
first "Zhiqiang" ,
initials "Z." } } ,
{
name
name {
last "Chen" ,
first "Zhu" ,
initials "Z." } } ,
{
name
name {
last "Wen" ,
first "Yumei" ,
initials "Y." } } } ,
affil
std {
affil "Chinese National Human Genome Center at Shanghai" ,
city "Shanghai" ,
country "China" ,
street "250 Bi Bo Road" ,
email "rensx at chgc.sh.cn" ,
fax "(8621)50801922" ,
phone "(8621)50801919" ,
postal-code "201203" } } ,
medium other ,
date
std {
year 2002 ,
month 11 ,
day 5 } } } } ,
title "Staphylococcus epidermidis ATCC 12228, complete genome" ,
molinfo {
biomol genomic ,
completeness complete } ,
create-date
std {
year 2002 ,
month 12 ,
day 20 } ,
update-date
std {
year 2003 ,
month 1 ,
day 2 } } ,
inst {
repr seg ,
mol dna ,
length 2499279 ,
topology circular ,
strand ds ,
ext
seg {
int {
from 0 ,
to 300786 ,
strand plus ,
id
gi 27314460 } ,
int {
from 60 ,
to 300241 ,
strand plus ,
id
gi 27314765 } ,
int {
from 60 ,
to 303210 ,
strand plus ,
id
gi 27315075 } ,
int {
from 60 ,
to 300891 ,
strand plus ,
id
gi 27315369 } ,
int {
from 60 ,
to 300028 ,
strand plus ,
id
gi 27315631 } ,
int {
from 60 ,
to 302822 ,
strand plus ,
id
gi 27315920 } ,
int {
from 60 ,
to 300697 ,
strand plus ,
id
gi 27316220 } ,
int {
from 60 ,
to 300274 ,
strand plus ,
id
gi 27316530 } ,
int {
from 60 ,
to 90801 ,
strand plus ,
id
gi 27316792 } } ,
hist {
assembly {
{
type partial ,
dim 2 ,
segs
denseg {
dim 2 ,
numseg 1 ,
ids {
gi 0 ,
gi 27314460 } ,
starts {
0 ,
0 } ,
lens {
300787 } ,
strands {
plus ,
plus } } } ,
{
type partial ,
dim 2 ,
segs
denseg {
dim 2 ,
numseg 1 ,
ids {
gi 0 ,
gi 27314765 } ,
starts {
300727 ,
0 } ,
lens {
300242 } ,
strands {
plus ,
plus } } } ,
{
type partial ,
dim 2 ,
segs
denseg {
dim 2 ,
numseg 1 ,
ids {
gi 0 ,
gi 27315075 } ,
starts {
600909 ,
0 } ,
lens {
303211 } ,
strands {
plus ,
plus } } } ,
{
type partial ,
dim 2 ,
segs
denseg {
dim 2 ,
numseg 1 ,
ids {
gi 0 ,
gi 27315369 } ,
starts {
904060 ,
0 } ,
lens {
300892 } ,
strands {
plus ,
plus } } } ,
{
type partial ,
dim 2 ,
segs
denseg {
dim 2 ,
numseg 1 ,
ids {
gi 0 ,
gi 27315631 } ,
starts {
1204892 ,
0 } ,
lens {
300029 } ,
strands {
plus ,
plus } } } ,
{
type partial ,
dim 2 ,
segs
denseg {
dim 2 ,
numseg 1 ,
ids {
gi 0 ,
gi 27315920 } ,
starts {
1504861 ,
0 } ,
lens {
302823 } ,
strands {
plus ,
plus } } } ,
{
type partial ,
dim 2 ,
segs
denseg {
dim 2 ,
numseg 1 ,
ids {
gi 0 ,
gi 27316220 } ,
starts {
1807624 ,
0 } ,
lens {
300698 } ,
strands {
plus ,
plus } } } ,
{
type partial ,
dim 2 ,
segs
denseg {
dim 2 ,
numseg 1 ,
ids {
gi 0 ,
gi 27316530 } ,
starts {
2108262 ,
0 } ,
lens {
300275 } ,
strands {
plus ,
plus } } } ,
{
type partial ,
dim 2 ,
segs
denseg {
dim 2 ,
numseg 1 ,
ids {
gi 0 ,
gi 27316792 } ,
starts {
2408477 ,
0 } ,
lens {
90802 } ,
strands {
plus ,
plus } } } } } } }
---
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