DDBJ Nucleotide Sequence
Submission System

1Outline of the submission
Open http://ddbj.nig.ac.jp/submission/and click "Create new submission"

1. Enter “Contact person”
Receive an email and click a link toactivate your submission

2. Enter “Hold date”

2

3. Enter “Submitter”

4. Enter “Reference”

35. Enter nucleotide sequences
Enter assembly information for TPA

6. Select template that matches to theannotation. You can choose input
annotation or upload annotation from file.

47. Input annotation or upload afile that contains annotation.

Repeat annotation check until
error is completely corrected.

8. Finish, you will soon receive an
email from DDBJ.

5

Start the submission from http://ddbj.nig.ac.jp/submission/
Please click here
to start thesubmission

6

1. Contact person
Contact person is the person who will make contact with DDBJ and DDBJ
users about the entry, in principle. One of the submitter can become acontact person.
Enter an email address of the contact person, who will contact
with DDBJ.

Enter a full name of contact person.
Select your region (country) name.
The country code is automatically selected at
fax/phone.
Enter fax number.

Please check, if fax is unavailable.
Enter telephone number.(If extension number isneeded, please fill the number at Ext.)
Enter institution name.
Enter URL, if you have any
Webpage (Optional).

Enter department name (Optional).

Enter zip code.
Enter state(or prefecture) name(optional).
Enter city name.

Enter street.

Please click “Next” after you fill the form.
An email will be automatically sent tocontact person’s email address.
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An email, which contains a link to start the submission, is automatically sent to thecontact person’s email address.
Subject: DDBJ: Starting the submission
Please click the link in the document of the email, then
To: mishima@nig.ac.jp
National Institute of Genetics
Dear Hanako Mishima

internet browser will be opened.
Or, if you cannot find the hyperlink in the email, please
copy the URL to browsers address bar and press enter.

Thank you for using DDBJ.
This email contains a link for proceeding of your nucleotide data submission.
Please click the link below, then, you can continue your registration.
http://ddbj.nig.ac.jp/submission/submissions/5036c6ee55d698c0ad000324/mail_con
firmation?token=47444d24e2106dd81a323f6ed559b715ec8cbbab
If you are not related person of the submission, please discard the email .
Note : You must activate your new submission within 1 hour. If you failed
to activate, please try again from the "Contact person" page.
Note : You can not reply to this mail.

If you encounter trouble while using this submission system, please send an
email to sakura-admin@ddbj.nig.ac.jp and let us know the browser's URL of
your submission.
Thank you,
DNA Data Bank of Japan8

2. Hold dateEnter hold date or select “Release immediately” on the page.
progress bar
Click the calendar icon and selectday that you would like to open the
nucleotide sequence.

Or click the check box , if you would
like to open the nucleotide
sequence immediately.

Please click “Next”
after you select thehold date.

• A day six months from today is highlighted when you click the calendar icon.
• You cannot select the several days on end or begin of the year as a hold datebecause DDBJ usually suspends the work to release the nucleotide sequences
during the days.
• The selectable hold date is limited within three yeas from today.
How to suspend/resume the submission
Please bookmark or save the URL of the page. You can resume
the submission from the bookmarked URL even if you close theinternet browser.

9How to use calendar

Move to previous month

You can select theyear from the list.

Move to next monthIf you would like toclose the calendar,
please click.

103. SubmitterEnter Submitter (s) on the page.

Contact person’s name isautomatically converted tosubmitter’s format.
You can correct the name, if you
need to change the name.

Please enter submitters abbreviation name based on a format of reference authors.
Format:last name[comma]initial of first name[period]initial of middle name [period]e.g.
Miyashita,Y.
Robertson,G.R.
Mishima-Tokai,H.
Kim,C.S.
Wang,Y.Q.
Please enter two or more submitters, if possible.

Click “Add”, then you can add
more submitter(s).
DDBJ recommend you toinclude two or more
submitters in the submission.
Submitters name will be
displayed in the flat fileaccording to the submittersorder of this page.

Please click “Next”
after you fill the form.

How to suspend/resume the submission
Please bookmark or save the URL of the page. You can resume
the submission from the bookmarked URL even if you close theinternet browser.

11

We would like to ask you to include two or more submitters.

We occasionally meet the situation where we cannot contact to the submitterin case of entries which have only one submitter. In our rule, submitter is
responsible for the data and only the submitter can update own entries. Without
contacting to the submitter, we cannot fulfill necessary corrections.
Of course, you can register your entries with only one submitter, but werecommend you to add more submitters, such as principal investigator,
to your entries.

12How to add a submitter

Please click “Add” and you willfind additional text field.
Please enter anothersubmitter and the email
address.

13

How to change the order of submitter
How to delete a submitter

move to down

Deletemove to up

14

4. ReferenceEnter reference information on the page.
Please enter primary citation on the 1st reference.

“Unpublished” is selected as default.

Please select “Unpublished”;
when you are planning or preparing for a manuscript,
when a manuscript is being submitted for publication,
when If you have not decided to prepare a paper whether
you would submit the paper or not.
Select “In press” when a paper is in press.

Select “Published” when a paper has been published.

Click “Add”, if you need to
add more reference(s).

A text form is changed according to a selection at the“Status”.

How to suspend/resume the submission
Please bookmark or save the URL of the page. You can resume
the submission from the bookmarked URL even if you close theinternet browser.

15

Status: Unpublished

You do not enter year. Current year is
automatically filled on the filed.
Enter the paper’s title.
Please fill appropriate title even if you
are not planning to prepare a paper.

Please enter reference author (1 person per 1 text box).
You can add more text field to click “Add authors” .
To remove the author, please click “X”.

Please click “Next”
after you fill the form.
Please enter submitters abbreviation name.
Format:last name[comma]initial of first name[period]initial of middle name [period]e.g.
Miyashita,Y.
Robertson,G.R.
Mishima-Tokai,H.
Kim,C.S.
Wang,Y.Q.
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Status: In press

Enter year

Please enter journals abbreviation name.
Autocomplete is available to enter the journal.

Enter the paper’s title.

Please enter reference author (1 person per 1 text box).
You can add more text field to click “Add authors” .
To remove the author, please click “X”.
Please enter submitters abbreviation name.
Format:last name[comma]initial of first name[period]initial of middle name [period]e.g.
Miyashita,Y.
Robertson,G.R.
Mishima-Tokai,H.
Kim,C.S.
Wang,Y.Q.
17

Enter year

Status: Published
Please enter journals abbreviation name.
Autocomplete is available to enter the journal.

Enter the paper’s title.

Enter volume, page of the paper. Please
fill DOI number, if available.

Please enter reference author (1 person per 1 text box).
You can add more text field to click “Add authors” .
To remove the author, please click “X”.
Please enter submitters abbreviation name.
Format:last name[comma]initial of first name[period]initial of middle name [period]e.g.
Miyashita,Y.
Robertson,G.R.
Mishima-Tokai,H.
Kim,C.S.
Wang,Y.Q.
18

Autocomplete function at the input field of journal name
You will see the candidate of journal’s name when you enter a full or part of the
beginning name of a journal. You can enter the journal’s abbreviation name by
select one from the list.

The system uses NLM Catalog for its Input dictionary. You can search journal’s
ISO abbreviation at NLM Catalog.

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e.g. How to search ISO abbreviation of “Journal of biological chemistry”

Open NLM Catalog on the internet browser and enter
keyword “journal name[journal]” and click search.

Click

Enter a full journal name[journal] to the search box and click
search.

20

Some candidate will be
displayed as a result.
Please click appropriate one
from the result.

21

You can obtain ISO
abbreviation of thejournal from here.

22

5.Sequence
Enter nucleotide sequence.
Assembly information is also needed for the case of TPA“Yes” is selected as a default.
Please keep it “Yes” when the
nucleotide sequence is not TPA.
Paste nucleotide
sequence.
The information entered at the page
"7.Annotatoin" is cleared if you change thenucleotide sequence at this page.

Or, you can upload
nucleotide
sequence file.

Please click “Next”
after you fill the form.

How to suspend/resume the submission
Please bookmark or save the URL of the page. You can resume
the submission from the bookmarked URL even if you close theinternet browser.

23

Nucleotide sequence that you can paste/upload
You can paste or upload nucleotide sequence consists of multiFASTA format.
Double slash(//) is not needed for separate the entries. Of course,
you can include double slash (//) as a separation mark of theentries.(e.g.1 & e.g.2)
This system automatically insert double slash (//) between entries
when the nucleotide sequence that contains no double slash (//) isentered.

Entry name is required to be described in less than 24 letters ofcharacters which do not contain [space], "[double-quote], ? [question], ¥, [back-slash].
Entry names must be unique in one submission.
If the same entry name are contained in the submission, you mustcorrect the entry name to avoid an error.
The sequence must consists of a, c, g, t, m, r, w, s, y, k, v, h, d, b, orn.
Spaces, numeric characters within the nucleotide sequence areautomatically removed.

e.g.1>CLN01
ggacaggctgccgcaggagccaggccgggagcaggtggtggaagacagacctgtaggtgg
aagaggcttcgggggagccggagaactgggccagaccccacaggtgcaggctgccctgtc
tgcgcttcagtcgtgggcgaagcctgaggaaaaagagagagaggctcaaggaagagagga
tgaggcaggagaatcgcttgaaccccggaggcggaggttgcagtgagccgagattacgcc
accgcactccagcctgggcgacagagtgagactccatctcaaaaaaaaaaaaaaaaaa>CLN02
ctcacacagatgctgcgcacaccagtggttgtaacaatgccgtttgcctccttcaggtct
gaagcctgaggtgcgctcgtggtcagtgaagagggcaaaaagagagagaggctcaaagga
tgcgcttcagtcgtgggcgaagcctgaggaaaaagagagagaggctcaaggaagagagga
tagtcattcatataaatttgaacacacctgctgtgcctagacaagtgtctttctgtaaga
gctgtaactctgagatgtgctaaataaaccctctttctcaaaaaaaaaaaaaaaa

e.g.2>CLN01
ggacaggctgccgcaggagccaggccgggagcaggtggtggaagacagacctgtaggtgg
aagaggcttcgggggagccggagaactgggccagaccccacaggtgcaggctgccctgtc
tgcgcttcagtcgtgggcgaagcctgaggaaaaagagagagaggctcaaggaagagagga
tgaggcaggagaatcgcttgaaccccggaggcggaggttgcagtgagccgagattacgcc
accgcactccagcctgggcgacagagtgagactccatctcaaaaaaaaaaaaaaaaaa//>CLN02
ctcacacagatgctgcgcacaccagtggttgtaacaatgccgtttgcctccttcaggtct
gaagcctgaggtgcgctcgtggtcagtgaagagggcaaaaagagagagaggctcaaagga
tgcgcttcagtcgtgggcgaagcctgaggaaaaagagagagaggctcaaggaagagagga
tagtcattcatataaatttgaacacacctgctgtgcctagacaagtgtctttctgtaaga
gctgtaactctgagatgtgctaaataaaccctctttctcaaaaaaaaaaaaaaaa//

Upper cases of the nucleotide residue id automatically converted
into lower cases.

24Sequence for TPA submission
Select “No” when the nucleotide sequence is notdetermined by yourselves and constructed byassembling primary entries publicized from
DDBJ/EMBL-Bank/GenBank.
The submission system switched to TPA mode.

Paste nucleotide
sequence.

Paste assembly
information for
construction of TPA
sequence.

Or, you can upload
nucleotide
sequence file.
Please click “Next”
after you fill theform.

Or, you can upload
assembly information file.

How to suspend/resume the submission
Please bookmark or save the URL of the page. You can resume the submission from thebookmarked URL even if you close the internet browser.

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Format of assembly Information for TPA submission
e.g.
FA01
BM123

Entry
Name

TPA_SPAN PRIMARY_IDENTIFIER
1-552
ZZ000001.1
553-705 ZZ000002.5
1-438
ZZ000010.1
377-695 ZZ000011.1
411-790 ZZ000021.12
790-1191 ZZ000022.0
Location of TPA
sequence

Accession number
with version ofprimary entry.

PRIMARY_SPAN
54872-55422
1-153
1-438
1-320
1-398
1-401

COMPLEMENTc“c” is designated whencomplementary regionof primary span is used.

Region of primary
entry.

The table means;
As for Entry name FA01
TPA sequence:1-552 corresponds to ZZ000001.1:54872-55422
TPA sequence:553-705 corresponds to ZZ000002.5:1-153
As for Entry name BM123
TPA sequence:1-438 corresponds to ZZ000010.1 :1-438
TPA sequence:377-695 corresponds to ZZ000011.1:complement(1-320)
TPA sequence:411-790 corresponds to ZZ000021.12:1-398
TPA sequence:790-1191 corresponds to ZZ000022.0 :1-401
Their correspondence is subject to the rule, “The sequence alignment rule between TPA and primary entries”
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Rule: Description of Assembly Information
 The 1st line must be[tab or space]TPA_SPAN[tab or space]PRIMARY_IDENTIFIER[tab or space]PRIMARY_SPAN[tab or space]COMPLEMENT

 Do not include null line(s) Entry name must be entered at the 1st column. Assembly information is separated with each entry at the line of entry name.
 TPA_SPAN:
X..Y or X-Y (X and Y are numeric, X<Y)
Location on TPA sequence is described.
e.g.
100..2000
100-2000 PRIMARY_IDENTIFIER:
accession number.version
Accession number with version of primary entry is described. Please use 0 for the version number if primary entry is notreleased.
e.g.
AB123456.1
AB987654.0
 PRIMARY_SPAN:
X..Y or X-Y (X and Y are numeric, X<Y)
The region from primary entry, which was used for construct TPA sequence, is described. The region must match to the
TPA_SPAN.
Please see "The sequence alignment rule between TPA and primary entries"
 COMPLEMENT:
null or cEnter "c" when complementary region is used from primary entry.
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6. Template① Taxonomic division① Please select a taxonomic division of the sequenced
organism. When nucleotide sequences have beenobtained from organelle, you should select one whosename includes ‘organelle’ to automatically add/organelle under source feature.
Available qualifier keys under source feature vary withthe selected taxonomic division.
If you cannot find an appropriate taxonomic division,
we recommend you to choose "Plant/Fungi(eukaryotes other than animals)" because almost②
qualifier keys are available in "Plant/Fungi" division.
(Link: taxonomic divisions,
http://www.ddbj.nig.ac.jp/sub/locus-e.html#division)② You will see an available annotation template.
Please select one and click "Input annotation".

Select "other" if you cannot find an appropriate
annotation template from the list . In the case,
you cannot use a spreadsheet-type editor forentering annotation.

How to suspend/resume the submission
Please bookmark or save the URL of the page. You canresume the submission from the bookmarked URL even if you
close the internet browser.

After the selection, please click "Input
annotation" and move to "7. Annotation" page.

The information entered at the"7.Annotatoin" page are disappeared if
you change the template at this page.

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7.Annotation
Four kinds of input method are available for spreadsheet-type annotation template.
Click "Edit" icon (recommended)
Double click a cell
Click edit icon at a qualifier
Click "Edit Column"
submission ID

Number of total
entries

You can select qualifier

Click "Edit" icon, then
you can edit the values
per entries
When you click Edit icon
on a qualifier, you can
edit value of the qualifierof whole entries.

Entry name(s) are
shown here.

Click "Edit column" makeyou possible to edit andbatch data input (copy &paste) per column.

You can edit a value by
double-click of each cell.

Link: Definition of Feature Key
 Definition of Qualifier key
 Organism qualifier CDS feature

How to suspend/resume the submission
Please bookmark or save the URL of the page. You can resume
the submission from the bookmarked URL even if you close theinternet browser.

29

e.g. How to enter annotation of 16S rRNA

1. Click here and add qualifier(s)2. Click "Edit" icon, then
you can edit the values
per entry.

Mandatory feature andqualifiers are automaticallyselected.

Location and product name ofrRNA feature are shown as
default value.
Check of the annotation
starts when you click"Confirm".
Link: Definition of Feature Key
 Definition of Qualifier key
 Organism qualifier CDS feature

You can add otherinformation by double
clicking a cell (freely
describable).

You cannot click "Next" if
the problems remains
after annotation check.
How to suspend/resume the submission
Please bookmark or save the URL of the page. You can resume
the submission from the bookmarked URL even if you close theinternet browser.

30

Select qualifier

To add qualifier(s), check the checkbox besidethe qualifier and click "Save".
To delete qualifier(s), uncheck it.
You cannot delete a qualifier if it is mandatory
for the annotation.

Available qualifiers vary depending on thekind of annotation template.

Link:
7.Annotation
Annotation screen when "Other" is selected at "Template"e.g. Input annotation of mitochondrial DNA

Link:
 Definition of Feature Key
 Definition of Qualifier key
 Organism qualifier CDS feature31

Edit feature/qualifier values of a entry

Select only for virus, environmental sample, etc.

Enter scientific nameof organism
Enter strain nameProduct name is displayed.
In the case(template for "16S rRNA
sequence"), it is not editable.

Whole region of the nucleotide
sequence is automatically put on thelocation of rRNA feature.
Please correct it, if you need.

Link:
7.Annotation
Annotation screen when "Other" is selected at "Template"e.g. Input annotation of mitochondrial DNA
How to input an organism name

Please click “Next” after you fill
the form.

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Annotation screen just after edit the 1st entry.

From the 2nd entry to the end,
please click "Edit" and fill annotation
like as the case of 1st entry.

Link: Definition of Feature Key
 Definition of Qualifier key
 Organism qualifier CDS feature

How to suspend/resume the submission
Please bookmark or save the URL of the page. You can resume
the submission from the bookmarked URL even if you close theinternet browser.

33

Annotation check starts when you click "Confirm"

Click "Confirm" when you
complete to enter the
annotation. After click, theannotation format checking
starts.

The "Next" will turned to beclickable when errors are solved.
You cannot click here if there
remains any problem after
annotation check.

Link:
Confirm => no errors
Confirm => You can proceed to the next step even though there are some warnings
Confirm => There are any errors
Direct links of the page that explains translation error s and warnings
How to suspend/resume the submission
Progress bar
Please bookmark or save the URL of the page. You can resume
final confirmation screen
the submission from the bookmarked URL even if you close theinternet browser.

34

Annotation screen when "Other" is selected at "Template"
You will see edit
window to edit theentry when click here.

You can add additional
information by clicking theicon when you need.

To edit the value of each qualifier,click the qualifier directly.

Click when you want to
add qualifier(s)You can edit value of aqualifier of whole entries.

Link: Definition of Feature Key
 Definition of Qualifier key
 Organism qualifier CDS feature

Click "Confirm" when you
complete to enter the
annotation. After click, theannotation format checking
starts.

In the template (other), you mustselect (add) feature and qualifier, which
are needed for the annotation of thesubmitted sequences, by yourself

When click here, the qualifier(s) selectedunder the source feature are copied tothe source feature of the next entries.

Click "Add feature" andselect feature from the list
to add feature key(s).

The "Next" will turned to be clickable
when errors are solved.
You cannot click here if there remains any
problem after annotation check.

How to suspend/resume the submission
Please bookmark or save the URL of the page. You
can resume the submission from the bookmarked
URL even if you close the internet browser.

35

e.g. Input annotation of mitochondrial DNA
3. Click "Edit" and enter annotation of the entry.

2. Click here if you would like to copy qualifier set, which are
selected at source feature, to the source feature of the next
entries to the end (Value of qualifier is not copied).

1. Choose qualifiers by clicking "Select Qualifier".
In the case, country, isolate, and organelle wereadded.
Link:
 Definition of Feature Key
 Definition of Qualifier key
 Organism qualifier CDS feature
Link:
Select qualifier
Edit feature/qualifier values of a entry

How to suspend/resume the submission
Please bookmark or save the URL of the page. You can resume
the submission from the bookmarked URL even if you close theinternet browser.

36

4. Click here and choose feature.

5. Select qualifier, which is added tothe selected feature, from here37

6. Click here and you will see input
field. Please correct location of the
field.

7. A window will open by clicking each qualifier. You
can enter or correct value on the window.
/codon_start is automatically set to "1" in the case of
CDS feature. You should correct the value if you need.

8. Add feature from here.

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Clicking "Confirm" on annotation screen
By clicking "Edit" icon, you can edit
annotation per each entry after you
choose feature and qualifier.
9. Please complete to enter the
annotation of the 1st entry.
Click trash icon to delete feature or
qualifier.

You have to enter all annotation fromthe next entry to the end.
Please click "Confirm" after you fill
the annotation, then, annotationchecking will start.
Link:
Confirm => no errors
Confirm => You can proceed to the next step even though there aresome warnings
Confirm => There are any errors
Direct links of the page that explains translation error s and warnings
Progress bar
final confirmation screen

The "Next" will turned to be clickable
when errors are solved.
You cannot click here if there remains any
problem after annotation check.
39

How to upload annotation froma tab-deliminated text-file① Taxonomic division① Please select a taxonomic division of the sequenced
organism. When nucleotide sequences have beenobtained from organelle, you should select one whosename includes ‘organelle’.
Available qualifier keys under source feature vary withthe selected taxonomic division.
If you cannot find an appropriate taxonomic division,
we recommend you to choose "Plant/Fungi(eukaryotes other than animals)" because almost
qualifier keys are available in "Plant/Fungi" division.
(Link: taxonomic divisions,
http://www.ddbj.nig.ac.jp/sub/locus-e.html#division)② Select “other” when you would like to upload
annotation by using a tab-deliminated text-file.

②
After the selection, please click"Upload annotation file".

The information entered at the"7.Annotatoin" page are disappeared if
you change the template at this page.
40

Submission by uploading the annotation file

Set an annotation file here.

Click "Upload & Confirm"
to start checking ofannotation file.

41

Annotation file that is able to be uploaded You can see some examples on ‘sample annotation file’ page.
 Please include only annotation section in annotation file.

 You cannot upload WGS, CON, AGP, EST, GSS, STS, HTG, HTC, TSA files. Please contact DDBJ
mass submission system (MSS) to submit such submission files.
 Information that you entered on the pages, "1. Contact person", "2. Hold date", "3. Submitter",and "4. Reference", are added in front of uploaded annotation file as COMMON section.
 When COMMON is included in the uploaded annotation file, if will be replaced withinformation obtained from "1. Contact person", "2. Hold date", "3. Submitter", and "4.
Reference." For TPA, you should not include PRIMARY_CONTIG section in annotation file.
PRIMARY_CONTIG section is automatically inserted to the uploaded annotation file byconverting information of the "5.Sequence" page.

Link: Definition of Feature Key
 Definition of Qualifier key
 Organism qualifier CDS feature

42

Example annotation file used for upload
COMMON

You do not have to include
the area to the annotation
file.
If it is included in the
annotation file, it will be
replaced with theinformation entered at thepages such as 1. Contact
person, 2. Hold date, 3.
Submitter, and 4. Reference

SUBMITTERREFERENCE

DATE
ENT01

You should include only thisregion (= section consists ofbiological features) inannotation file.

sourceCDS

1..2878

217..1104

3'UTR

1105..2878

polyA_signal2857..2862

polyA_site

ENT02

sourceCDS

contact

Hanako Mishima

ab_nameMishima,H.

ab_name

Yamada,T.

ab_namePark,C.S.

ab_name

Liu,G.Q.

email

mishima@ddbj.nig.ac.jp

phone

81-55-981-6853

fax

81-55-981-6849

institute

National Institute of Genetics

department

DNA Data Bank of Japancountry

Japan

state

Shizuokacity

MishimastreetYata 1111

zip

411-8540

ab_nameMishima,H.

ab_name

Yamada,T.

ab_namePark,C.S.

ab_name

Liu,G.Q.

title

Aquaporin genes

year

2012

statusUnpublishedhold_date20131130

organism

Homo sapiens

isolateFA01

mol_typemRNA

tissue_type

liver

gene

AQP9

productaquaporin 9organism

Shigella flexneri

strainBM123

mol_type

genomic DNA

gene

APQZ

producttransl_tableaquaporin Z
11codon_start

2

2878

1..1409<1..1051

43

"Upload & Confirm" => no error

Annotation appears under the button when annotation file
check is completed.
The COMMON is replaced with the values entered at thepages of 1.Contact person - 4.Reference.
"Next" turns to be clickable when there is no error.
"Next" turns to be clickable even if there is some warning. You
should correct the annotation if needed.

Link：
final confirmation screen

How to suspend/resume the submission
Please bookmark or save the URL of the page. You can resume
the submission from the bookmarked URL even if you close theinternet browser.

44

"Upload & Confirm" => Error/Warning occurred
Please correct annotation file and upload
it from here and click "Upload &Confirm" until errors are disappeared.

"Next" turns to be clickable when
there is no error. "Next" turns to beclickable even if there is somewarning. You can click "Next" if there
are no problems in the annotation.

Click to see a page of detailed
description of the error.

You can move to the error line ofannotation file below by clicking theline number.
Error/Warning message

Annotation file is displayed here. Errorline is indicated in red.

How to suspend/resume the submission
Please bookmark or save the URL of the page. You can resume
the submission from the bookmarked URL even if you close theinternet browser.

45

final confirmation screen
You can browse theinformation of pages 1
to 7 in text format.

The screen will appear after
you click "Next".

Please click either one if there is
no problem.

Please describe here if
there are any otherinformation when needed.

How to suspend/resume the submission
Please bookmark or save the URL of the page. You can resume
the submission from the bookmarked URL even if you close theinternet browser.

Link：
Annotation check starts when you click "Confirm"
Clicking "Confirm" on annotation screen (when Template: other was selected)"Upload & Confirm" => no error

46

8. Finish

Please bookmark the page. You canbrowse the page from thebookmark for a certain period eventhough you close the browser.

The submission files are now transferred to DDBJ. The
submission is completed when you see the finish screen.
An email will be sent to contact person's email address.
You can download the files in DDBJ
registration format. Please download
and save them.
You do not have to send them to DDBJ
because the files were automaticallytransferred to DDBJ server.

If you meet any problems
regarding of the tool, please email
to the address.

Link:
final confirmation screen
47

You will receive an email when submission completed
From: sakura-admin@ddbj.nig.ac.jp
Subject: DDBJ: Web submission completed
Contact person : mishima@nig.ac.jp
Hanako Mishima
National Institute of Genetics
DDBJ center, DDBJ
1111 Yata
Mishima, Shizuoka, 411-8540
Japan
Thank you very much for choosing DDBJ for data submission.
We have received your data. We will soon check and annotate them on the basis of
the manual and rules common to the DDBJ, EMBL-Bank, and GenBank.
If you do not hear from DDBJ after 5 working days after receiving this notice,please contact us at the following address indicating your Entry Name.
Email address: sakura-admin@ddbj.nig.ac.jp
Sincerely,
DNA Data Bank of JapanDDBJ Center
National Institute of Genetics
Research Organization of Informationand Systems
Mishima, Shizuoka 411-8540, Japanfax:+81-55-981-6849[Hold-date]2013-03-29[Entry ID]
5065382e55d69849870005fe.entry01
5065382e55d69849870005fe.entry02

Link:
8. Finish

48

Illustrations of text input field

49

Edit icon at each qualifier

You can edit each value per column ofannotation table.

To copy the same value after
the entry, click "Copy".

Click "Save" after you edit thevalue.

Link:
7.Annotation
Annotation screen when "Other" is selected at "Template"e.g. Input annotation of mitochondrial DNA
50

Edit column

You can edit each value per column ofannotation table.

You can edit directly on the text area or
copy & paste the data from Excel or text
editor.
Please use line feed (or press return key)
to separate entry.

Click "Save" after edit/enterthe value.
Link:
7.Annotation
Annotation screen when "Other" is selected at "Template"e.g. Input annotation of mitochondrial DNA

51

Double-click a cell
(Click qualifier for "Other" template)

A window will open when you double-click acell (When you select "other" at template page,
you should click each qualifier, then you can see
the same window). Please edit or enter value
against the input field.

Click "Save" after edit/enterthe value.

Link:
7.Annotation
Annotation screen when "Other" is selected at "Template"e.g. Input annotation of mitochondrial DNA

52

How to input organism nameEnter a correct scientific name here.
When you type a name, candidates areautomatically searched from the
GenBank taxonomy database anddisplayed on the screen. Please selectone from the list and click "OK".

Please click "Edit"

53

How to input an organism not registered intaxonomy database
When you enter a new organism, which has notbeen registered to the GenBank taxonomy
database, you must select "Category" and input
information about the organism such as
taxonomic lineage, valid publication, and so on.
Link: http://www.ddbj.nig.ac.jp/sub/ref8-e.html#deasy

After input of an organism name, genetic code
(must be an integer) is automatically entered tothe text box when the organism name isincluded in the GenBank taxonomy database.
You must manually enter a genetic code (e.g. 1
for universal, 11 for Bacteria, 2 for vertebrate
mitochondrion, 5 for invertebrate
mitochondrion) when the organism name is notregistered to the taxonomy database and an
integer is not automatically entered.

54

Category: The name is valid but not registered in taxonomy database
ExamplePlease select PMID/DOI/Accession/noID
PMID
Enter PubMed unique identifier of the
publication.

Please enter taxonomic lineage. You can search
it by NCBI tax search.

DOIEnter digital object identifier of the publication.
Accession number
Please enter accession number(s) if the sameorganism has been registered to DDBJ/EMBLBank/GenBank.
noID
When the publication has no id, please select"noID" and describe the information of the
publication such as title, authors, year, volume,
pages, and journal name.

Please describe helpful information regarding
the organism (optional).

Link:
http://www.ddbj.nig.ac.jp/sub/ref8-e.html#deasy

55

Category: Species is not identified

Please enter taxonomic lineage (Optional). You
can search it by NCBI tax search.

Link:
http://www.ddbj.nig.ac.jp/sub/ref8-e.html#deasy

56

Category: Pathogenic virus

Please enter taxonomic lineage (Optional). You
can search it by NCBI tax search.

Link:
http://www.ddbj.nig.ac.jp/sub/ref8-e.html#deasy
57

Category: Valid subspecies or variety not registered in taxonomy database

Please select PMID/DOI/Accession/noID

PMID
Enter PubMed unique identifier of the
publication.

Please enter taxonomic lineage. You can search
it by NCBI tax search.

DOIEnter digital object identifier of the publication.
Accession number
Please enter accession number(s) if the sameorganism has been registered to DDBJ/EMBLBank/GenBank.
noID
When the publication has no id, please select"noID" and describe the information of the
publication such as title, authors, year, volume,
pages, and journal name.

Please describe helpful information regarding
the organism (optional).

Link:
http://www.ddbj.nig.ac.jp/sub/ref8-e.html#deasy

58

Category: Proposing the name for the novel species

You should enter a tentative name at/organism when proposing a novel species.

Please enter a proposed name that will bereported by the paper.

Please enter taxonomic lineage. You can search
it by NCBI tax search.

Please describe helpful information regarding
the organism (optional).

Link:
http://www.ddbj.nig.ac.jp/sub/ref8-e.html#deasy

59

Category: Obtained by direct molecular isolation from environmental sample

Please enter taxonomic lineage. You can search
it by NCBI tax search.

Please enter helpful information
regarding the sample (optional)

Link:
http://www.ddbj.nig.ac.jp/sub/ref8-e.html#deasy
60

Category: Artificially constructed or synthesized sequence

Please enter helpful information
regarding the synthetic sequence(optional)

Link:
http://www.ddbj.nig.ac.jp/sub/ref8-e.html#deasy
61

Link to the pages for detailed description of errors & warnings

You can see detailed explanation of Errors and Warning at;
http://www.ddbj.nig.ac.jp/sub/validator-j.html

Regarding the errors and warnings about amino acid translation of CDS feature,
you can see their explanation at;
http://www.ddbj.nig.ac.jp/sub/validator-j.html#TC

Please refer the following links for preparation of annotation.
• Definition of Feature Key• Definition of Qualifier key• Organism qualifier• CDS feature

62

Direct links of the page that explains translation errors and warnings

Message[WARNING] 'codon_start' qualifier should be selected. The value is automatically set 1.
[WARNING] 'transl_table' qualifier should be selected. The value is automatically set 1.
[WARNING] Amino acid of 'transl_except' qualifier [#Value] is not [Met].
[ERROR] Untranslatable codon [#Codon] is found in the sequence range.
[ERROR] First codon [#Codon] is not a start codon.
[ERROR] Final codon [#Codon] is not a stop codon.
[ERROR] Stop codon '*' is found in the range.
[ERROR] Description of Location [#location of CDS feature] is illegal.
[ERROR] 'codon_start' qualifier is duplicated. The value is automatically set 1.
[ERROR] 'codon_start' qualifier has invalid value [#Value].
[ERROR] 'transl_table' qualifier is duplicated. The value is automatically set 1.
[ERROR] 'transl_table' qualifier has invalid value [#Value].
[ERROR] Amino acid abbreviation [#abbreviation] in 'transl_except' qualifier is illegal.
[ERROR] 'transl_except' qualifier has invalid value [#Value].
[ERROR] Location of 'transl_except' qualifier [#Value] is overlapped.
[ERROR] Location of 'transl_except' qualifier [#Value] is invalid.
[ERROR] Base range of 'transl_except' qualifier [#Value] is mismatched in reading frame.
[ERROR] Amino acid of 'transl_except' qualifier [#Value] is not changed from conceptual translation.
[ERROR] Amino acid of 'transl_except' qualifier [#Value] is not [TERM].
[ERROR] Stop codon is specified by 'transl_except' qualifier [#Value] in mid of CDS location.
[ERROR] Entry [#Entry name] is NOT found in sequence entries.
[FATAL] Proper 'Codon Table' is not found in 'src' folder.
[FATAL] Proper 'Amino Table' is not found in 'src' folder.
[FATAL] Unable to execute Translation.

Link
http://www.ddbj.nig.ac.jp/sub/validator-j.html#TC22
http://www.ddbj.nig.ac.jp/sub/validator-j.html#TC23
http://www.ddbj.nig.ac.jp/sub/validator-j.html#TC24
http://www.ddbj.nig.ac.jp/sub/validator-j.html#TC18
http://www.ddbj.nig.ac.jp/sub/validator-j.html#TC19
http://www.ddbj.nig.ac.jp/sub/validator-j.html#TC20
http://www.ddbj.nig.ac.jp/sub/validator-j.html#TC21
http://www.ddbj.nig.ac.jp/sub/validator-j.html#TC04
http://www.ddbj.nig.ac.jp/sub/validator-j.html#TC05
http://www.ddbj.nig.ac.jp/sub/validator-j.html#TC06
http://www.ddbj.nig.ac.jp/sub/validator-j.html#TC07
http://www.ddbj.nig.ac.jp/sub/validator-j.html#TC08
http://www.ddbj.nig.ac.jp/sub/validator-j.html#TC09
http://www.ddbj.nig.ac.jp/sub/validator-j.html#TC10
http://www.ddbj.nig.ac.jp/sub/validator-j.html#TC11
http://www.ddbj.nig.ac.jp/sub/validator-j.html#TC12
http://www.ddbj.nig.ac.jp/sub/validator-j.html#TC13
http://www.ddbj.nig.ac.jp/sub/validator-j.html#TC14
http://www.ddbj.nig.ac.jp/sub/validator-j.html#TC15
http://www.ddbj.nig.ac.jp/sub/validator-j.html#TC16
http://www.ddbj.nig.ac.jp/sub/validator-j.html#TC17
http://www.ddbj.nig.ac.jp/sub/validator-j.html#T01
http://www.ddbj.nig.ac.jp/sub/validator-j.html#T02
http://www.ddbj.nig.ac.jp/sub/validator-j.html#T03

63

Confirm => no errors

It means that you can click"Next" button.

Annotation file (DDBJ
acceptable format) appears at
the bottom of the page.

"Next" button is changed to beclickable and you can move tothe next process.

Link:
Annotation check starts when you click "Confirm"
Clicking "Confirm" on annotation screen (when "other" is selected at "Template")
final confirmation screen
64Error/warning messages are displayed beneath input area
Click the icon to open a page that
contains detailed description.

Click the line number to jump to
the error-occurring line of theannotation file.

Error/Warning message

Annotation file (DDBJ acceptable format) is
appeared at the bottom of the page.
Error lines are displayed in red.
In order to correct error, please scroll-up thescreen, and edit entry at which error occurred onannotation input field.
Please click "Confirm" after you correct the errors.

Link:
Annotation check starts when you click "Confirm"
Clicking "Confirm" on annotation screen (when "other" is selected at "Template")
65Confirm => You can proceed to the next step even though there are some warnings

It means that you can click"Next" button.

In the case, there is a warning
regarding the name ofsubmitter.
In some cases, "Next" button changes
to be clickable, even though there aresome warnings.

Link:
Annotation check starts when you click "Confirm"
Clicking "Confirm" on annotation screen (when "other" isYou can click "Next" if you believe that
there is no problem in the input data.

selected at "Template")

final confirmation screen

66Confirm => There are any errors

Error messages areshown here.

Link:
Errors/Warnings occurred in entry
Errors/Warnings occurred in Submitter
Errors/Warnings occurred in Reference"Next" button will not beclickable, if there are some errors.

Annotation check starts when you click "Confirm"
Clicking "Confirm" on annotation screen (when "other" isselected at "Template")

67

Errors/Warnings occurred in entry

In this example, a value of lat_long at
ENT01 is corrected.

Link:
Annotation check starts when you click "Confirm"
Clicking "Confirm" on annotation screen (when "other" isselected at "Template")

Confirm => There are any errors
68Scroll up the page and double click the cellof lat_lon at ENT01 and edit the value.

69

Errors/Warnings occurred in Submitter

Click "3.Submitter" at progress bar.
Please correct submitter at"3.Reference page" and click "Next".

You can return by clicking"7.Annotation".

Click "3.Submitter" at progress bar.
You can move to "3.Submitter" page. Please correct submitter and click"Next" at the bottom of the page.
Please click "7.Annotation" at progress bar to return to annotation screen.
Link:
Progress bar
Annotation check starts when you click "Confirm"
Clicking "Confirm" on annotation screen (when "other" isselected at "Template")"Upload & Confirm" => Error/Warning occurred
Confirm => There are any errors
70Errors/Warnings occurred in Reference

Click "4.Reference" at progress bar.
Please correct reference at"4.Reference page" and click "Next".

You can return by clicking"7.Annotation".

Click "4.Reference" at progress bar.

You can move to "4.Reference" page. Please correct reference and click"Next" at the bottom of the page.
Please click "7.Annotation" at progress bar to return to annotation screen.

Link:
Progress bar
Annotation check starts when you click "Confirm"
Clicking "Confirm" on annotation screen (when "other" isselected at "Template")"Upload & Confirm" => Error/Warning occurred
Confirm => There are any errors
71

Progress bar

 You can go back to previous page by clicking each page name. Pleaseclick "Next" at the bottom of each page if you correct the value at theprevious page.
 The annotation is disappeared if you change nucleotide sequence at"5.Sequence" page.
 The annotation is also disappeared if you change kind of template at"6.Template" page.

Link:
2.Hold date
Errors/Warnings occurred in Submitter
Errors/Warnings occurred in Reference
Annotation check starts when you click "Confirm"
Clicking "Confirm" on annotation screen (when "other" isselected at "Template")"Upload & Confirm" => Error/Warning occurred
Confirm => There are any errors
72