Transcript of DDBJ Nucleotide Sequence Submission System の紹介
- 1. DDBJ Nucleotide Sequence Submission System Takehide Kosuge,
Ph.D DDBJ DDBJ, Annotator 2014612 29 DDBJing (DDBJ) 1
- 2. 2014612 29 DDBJing (DDBJ) 2 2 3 4 DDBJ(flat file) 5 6 7 () 8
CDSLocation 9 DDBJ 10 11 12 Web 13 DDBJ Nucleotide Sequence
Submission System 14 Submission System 15 19 20 1. Contact person
21 22 2. Hold date 23 3. Submitter 24 4. Reference 25 5. Sequence
26 27 6. Template 28 7. Annotation 29 7. Annotation Templateother
30 Confirm"Next" 31 8. Finish 32 33 34 35 36 2. Submitter 37 4.
Reference Unpublished 38 In press 39 Published 40 JournalJournal 41
: Journal of biological chemistry 42 TPA 43 TPA Assembly
Information 44 Assembly Information 45 Qualifier 46 Edit Column 47
Template: other (qualifier) 48 49 genetic code 50 51 Category: 52
Viruses/Phages 53 Environmental Samples 54 Artificial construct 55
A known species but unregistered in taxonomy database 56 Not found
in taxonomy database, but already registered in other sequence data
57 A novel species to be proposed in the paper 58 annotation file
upload 59 Upload annotation file 60 annotation file 61 62 Upload
& Confirm Error 63 Error/Warning 64 Confirm error 65 error 66
warning 67 SubmitterReferenceerror 68 Error/Warning 69 CDS 70 16S
rRNA 71 COI 77 annotation 79
- 3. DDBJ Nucleotide Sequence Submission System (DDBJ) DDBJ Mass
Submission System (MSS) GenBank ENA DDBJ GenBank ENA E- mail INSDC*
*INSDC =International Nucleotide Sequence Database Collaboration
http://www.insdc.org/ 2014612 29 DDBJing (DDBJ) 3
- 4. (email) (email DDBJ (annotator) DDBJ (Submitter(s)) 2014612
29 DDBJing (DDBJ) 4
- 5. DDBJ(flat file) DEFINITION () DDBJ LOCUS ABxxxxxx 450 bp
mRNA linear HUM 01-JUN-2014 DEFINITION Homo sapiens GAPD mRNA for
glyceraldehyde-3-phosphate dehydrogenase, partial cds. ACCESSION
ABxxxxxx VERSION ABxxxxxx.1 KEYWORDS . SOURCE Homo sapiens ORGANISM
Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates;
Haplorrhini; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to
450) AUTHORS Mishima,H. and Shizuoka,T. TITLE Direct Submission
JOURNAL Submitted (30-NOV-2013) to the DDBJ/EMBL/GenBank databases.
Contact:Hanako Mishima National Institute of Genetics, DNA Data
Bank of Japan; Yata 1111, Mishima, Shizuoka 411-8540, Japan
REFERENCE 2 AUTHORS Mishima,H., Shizuoka,T. and Fuji,I. TITLE
Glyceraldehyde-3-phosphate dehydrogenase expressed in human liver
JOURNAL Unpublished (2013) COMMENT Human cDNA sequencing project.
FEATURES Location/Qualifiers source 1..450 /chromosome="12"
/clone="GT200015" /clone_lib="lambda gt11 human liver cDNA
(GeneTech. No.20)" /map="12p13" /mol_type="mRNA" /organism="Homo
sapiens" /tissue_type="liver" CDS 86..>450 /codon_start=1
/gene="GAPD" /product="glyceraldehyde-3-phosphate dehydrogenase"
/protein_id="BAA12345.1" /transl_table=1
/translation="MAKIKIGINGFGRIGRLVARVALQSDDVELVAVNDPFITTDYMT
YMFKYDTVHGQWKHHEVKVKDSKTLLFGEKEVTVFGCRNPKEIPWGETSAEFVVEYTG
VFTDKDKAVAQLKGGAKKV" BASE COUNT 102 a 119 c 131 g 98 t ORIGIN 1
cccacgcgtc cggtcgcatc gcacttgtag ctctcgaccc ccgcatctca tccctcctct
61 cgcttagttc agatcgaaat cgcaaatggc gaagattaag atcgggatca
atgggttcgg 121 gaggatcggg aggctcgtgg ccagggtggc cctgcagagc
gacgacgtcg agctcgtcgc 181 cgtcaacgac cccttcatca ccaccgacta
catgacatac atgttcaagt atgacactgt 241 gcacggccag tggaagcatc
atgaggttaa ggtgaaggac tccaagaccc ttctcttcgg 301 tgagaaggag
gtcaccgtgt tcggctgcag gaaccctaag gagatcccat ggggtgagac 361
tagcgctgag tttgttgtgg agtacactgg tgttttcact gacaaggaca aggccgttgc
421 tcaacttaag ggtggtgcta agaaggtctg // Feature Location /Qualifier
Feature = source, CDS Location = Qualifier = feature / /clone,
/gene, /product DDBJ (flat file)
http://www.ddbj.nig.ac.jp/sub/ref10-j.html 2014612 29 DDBJing
(DDBJ) 5
- 6. Submit submission (PC1024 1024DDBJ ) FirefoxChrome IE10IE11
Safari IE8 DDBJ Mass Submission System () 1024 (30)Feature ( 500 kb
) ESTSTSTSAHTCGSSHTGWGSCON(AGP)
(http://www.ddbj.nig.ac.jp/sub/data_categories-j.html, Division)
2014612 29 DDBJing (DDBJ) 6
- 7. (DDBJEmail) () hold date () or Reference ()
(vectorlinkeradaptor) (/strain)(/tissue_type) (mRNA or genomic DNA
or ) (location) protein-coding sequence (CDS) gene
symbol(/gene)(/product) 2014612 29 DDBJing (DDBJ) 7
- 8. () http://www.ddbj.nig.ac.jp/sub/example-j.html () DDBJ
2014612 29 DDBJing (DDBJ) 8
- 9. CDSLocation Feature key ()
http://www.ddbj.nig.ac.jp/sub/ref5-j.html Qualifier key ()
http://www.ddbj.nig.ac.jp/sub/ref6-j.html
http://www.ddbj.nig.ac.jp/sub/example-j.html
http://www.ddbj.nig.ac.jp/sub/ref8-j.html (CDS)
http://www.ddbj.nig.ac.jp/sub/cds-j.html Location ()
http://www.ddbj.nig.ac.jp/sub/ref9-j.html 2014612 29 DDBJing (DDBJ)
9
- 10. DDBJ Submission ( SAKURA ) 16S rRNA, 1 CDS, Influenza A
virus feature keyqualifier key Multi-fasta feature keyqualifier key
DDBJ 2014612 29 DDBJing (DDBJ) 10
- 11. http://www.ddbj.nig.ac.jp/ DDBJ" " 2014612 29 DDBJing
(DDBJ) 11
- 12. DDBJ Nucleotide Sequence Submission System 2014612 29
DDBJing (DDBJ) 12
- 13. Web "" 2014612 29 DDBJing (DDBJ) 13
- 14. DDBJ Nucleotide Sequence Submission System Create new
submission Firefox Chrome SafariIE10IE11 IE8 2014612 29 DDBJing
(DDBJ) 14
- 15. Submission System 1. Contact person 2. Hold date "Create
new submission" 2014612 29 DDBJing (DDBJ) 15
- 16. 3. Submitter 4. Reference 2014612 29 DDBJing (DDBJ) 16
- 17. 5. TPAAssembly Information 6. upload 2014612 29 DDBJing
(DDBJ) 17
- 18. 7. upload 8. 2014612 29 DDBJing (DDBJ) 18
- 19. 2014612 29 DDBJing (DDBJ) 19
- 20. : 2014612 29 DDBJing (DDBJ) 20
- 21. 1. Contact person Email, Fax, Phone Ne DDBJ full name
faxphone FAX FAX ( ) () URL() () 2014612 29 DDBJing (DDBJ) 21
- 22. Subject: DDBJ: Starting the submission To:
mishima@nig.ac.jp National Institute of Genetics Dear Hanako
Mishima 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_confirmation?token=47444d24e210
6dd81a323f6ed559b715ec8cbbab 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 ddbjsub@ddbj.nig.ac.jp
and let us know the browser's URL of your submission. Thank you,
DNA Data Bank of Japan 1 "1.Contact person" Email EmailNext URL
2014612 29 DDBJing (DDBJ) 22
- 23. 2. Hold date (Hold date) 6 DDBJ 3 Ne 2014612 29 DDBJing
(DDBJ) 23
- 24. 3. Submitter Contact person Submitter () : last
name[comma]first name [period]middle name [period] : Miyashita,Y.
Robertson,G.R. Mishima-Tokai,H. Kim,C.S. Wang,Y.Q. Add (2.
Submitter) DDBJ Ne URL URL (Submitter)
http://www.ddbj.nig.ac.jp/sub/submitter-j.html 1 () 2014612 29
DDBJing (DDBJ) 24
- 25. 4. Reference Reference (Primary citation)reference
Unpublished Unpublished In press Published UnpublishedIn
pressPublished ( 4. Reference) Reference URL URL Reference
http://www.ddbj.nig.ac.jp/sub/reference2-j.html : last
name[comma]first name [period]middle name [period] : Miyashita,Y.
Robertson,G.R. Mishima-Tokai,H. Kim,C.S. Wang,Y.Q. Ne 2014612 29
DDBJing (DDBJ) 25
- 26. 5. Sequence upload Yes "YES" "No." TPA ( TPA ) Ne URL URL
7.Annotation 2014612 29 DDBJing (DDBJ) 26
- 27. >CLN01
ggacaggctgccgcaggagccaggccgggagcaggtggtggaagacagacctgtaggtgg
aagaggcttcgggggagccggagaactgggccagaccccacaggtgcaggctgccctgtc
tgcgcttcagtcgtgggcgaagcctgaggaaaaagagagagaggctcaaggaagagagga
tgaggcaggagaatcgcttgaaccccggaggcggaggttgcagtgagccgagattacgcc
accgcactccagcctgggcgacagagtgagactccatctcaaaaaaaaaaaaaaaaaa
>CLN02
ctcacacagatgctgcgcacaccagtggttgtaacaatgccgtttgcctccttcaggtct
gaagcctgaggtgcgctcgtggtcagtgaagagggcaaaaagagagagaggctcaaagga
tgcgcttcagtcgtgggcgaagcctgaggaaaaagagagagaggctcaaggaagagagga
tagtcattcatataaatttgaacacacctgctgtgcctagacaagtgtctttctgtaaga
gctgtaactctgagatgtgctaaataaaccctctttctcaaaaaaaaaaaaaaaa >CLN01
ggacaggctgccgcaggagccaggccgggagcaggtggtggaagacagacctgtaggtgg
aagaggcttcgggggagccggagaactgggccagaccccacaggtgcaggctgccctgtc
tgcgcttcagtcgtgggcgaagcctgaggaaaaagagagagaggctcaaggaagagagga
tgaggcaggagaatcgcttgaaccccggaggcggaggttgcagtgagccgagattacgcc
accgcactccagcctgggcgacagagtgagactccatctcaaaaaaaaaaaaaaaaaa //
>CLN02
ctcacacagatgctgcgcacaccagtggttgtaacaatgccgtttgcctccttcaggtct
gaagcctgaggtgcgctcgtggtcagtgaagagggcaaaaagagagagaggctcaaagga
tgcgcttcagtcgtgggcgaagcctgaggaaaaagagagagaggctcaaggaagagagga
tagtcattcatataaatttgaacacacctgctgtgcctagacaagtgtctttctgtaaga
gctgtaactctgagatgtgctaaataaaccctctttctcaaaaaaaaaaaaaaaa //
Multi-FASTA() Entry name ()( "?) Entry name Entry name Entry name
// ( 2 ) // // a, c, g, t, m, r, w, s, y, k, v, h, d, b, or n
2014612 29 DDBJing (DDBJ) 27
- 28. 6. Template template "Input annotation" 16S rRNA other
7.Annotation template"Input annotation" upload upload annotation
file upload URL URL 2014612 29 DDBJing (DDBJ) 28
- 29. 7. Annotation : Edit (c) (a)Qualifier (b)Edit Column copy
& paste : Qualifier featurequalifier "6.Template"other
source"Select Qualifier"Qualifier source"Select Qualifier"Qualifier
"Edit" ConfirmError ConfirmErrorNext Next "Edit" a. Qualifier
(Qualifier ) b. Edit Column(Edit Column) c. ( Template: other
(qualifier) ) : "Next" URL URL Entry name : annotation Confirm
2014612 29 DDBJing (DDBJ) 29
- 30. : "Edit" "Comment" (b) Qualifierlocation URL URL (a)
source"Select Qualifier"source Qualifier "Edit"source Add
featurefeaturefeatureQualifier feature"Select Qualifier" qualifier
featurelocationqualifier feature "Confirm"Error
"Confirm"Error"Next" "Next" : featureAdd feature CDS : feature
location, qualifier : "Select Qualifier" qualifier : annotation
Confirm : "Next" source "Edit" a. sourcequalifier ( Qualifier ) b.
locationqualifier( Template: other (qualifier) ) 2014612 29 DDBJing
(DDBJ) 30 7. Annotation Templateother
- 31. Confirm"Next" "Submit to DDBJ" "8. Finish" Next
"5.Sequence""6.Template" "7.Annotation" "7.Annotation" Confirm Next
2014612 29 DDBJing (DDBJ) 31
- 32. 8. Finish DDBJ () DDBJ DDBJ DDBJ URL 2014612 29 DDBJing
(DDBJ) 32
- 33. 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 ID. Email address:
ddbjsub@ddbj.nig.ac.jp Sincerely, DNA Data Bank of Japan DDBJ
Center National Institute of Genetics Research Organization of
Information and Systems Mishima, Shizuoka 411-8540, Japan fax:
+81-55-981-6849 [Hold-date] 2013-03-29 [Entry ID]
5065382e55d69849870005fe.entry01 5065382e55d69849870005fe.entry02
From: ddbjsub@ddbj.nig.ac.jp Subject: DDBJ: Web submission
completed 2014612 29 DDBJing (DDBJ) 33
- 34. multi-fastaannotation vectoradapterlinkerprimer
VecScreen(http://ddbj.nig.ac.jp/vecscreen/) genetic code CDS
:genetic code CDS location
Location(http://www.ddbj.nig.ac.jp/sub/ref9-j.html) ; CDS feature
(http://www.ddbj.nig.ac.jp/sub/cds- j.html "MGA:No entry name is
found other than [ COMMON ], without feature [ DATATYPE/type=MGA
]." /organism/mol_type"Confirm" annotation"Confirm" 2014612 29
DDBJing (DDBJ) 34
- 35. 2014612 29 DDBJing (DDBJ) 35
- 36. "Next" "5.Sequence" "6.Template" 2014612 29 DDBJing (DDBJ)
36
- 37. 2. Submitter "Add" Add 2014612 29 DDBJing (DDBJ) 37
- 38. 4. Reference Unpublished Year 1 Add authors X : last
name[comma]first name [period]middle name [period] : Miyashita,Y.
Robertson,G.R. Mishima-Tokai,H. Kim,C.S. Wang,Y.Q. Ne 2014612 29
DDBJing (DDBJ) 38
- 39. In press(ISO abbreviation) :JournalJournal Year 1 Add
authors X : last name[comma]first name [period]middle name [period]
: Miyashita,Y. Robertson,G.R. Mishima-Tokai,H. Kim,C.S. Wang,Y.Q.
4. Reference In press 2014612 29 DDBJing (DDBJ) 39
- 40. 4. Reference Published Year VolumePage DOI : last
name[comma]first name [period]middle name [period] : Miyashita,Y.
Robertson,G.R. Mishima-Tokai,H. Kim,C.S. Wang,Y.Q. In press(ISO
abbreviation) :JournalJournal 1 Add authors X 2014612 29 DDBJing
(DDBJ) 40
- 41. JournalJournal Journal Namefull name ISO Abbreviation NLM
Catalog ISO Abbreviation NLM Catalog 2014612 29 DDBJing (DDBJ)
41
- 42. : Journal of biological chemistry NLM
Catalog(http://www.ncbi.nlm.nih.gov/nlmcatalog/) [journal] Search
journal of biological chemistry[journal] ISO Abbreviation 2014612
29 DDBJing (DDBJ) 42
- 43. TPA upload "No" TPA TPA( ) Assembly Information upload URL
URL Next 2014612 29 DDBJing (DDBJ) 43
- 44. TPA Assembly Information TPA_SPAN PRIMARY_IDENTIFIER
PRIMARY_SPAN COMPLEMENT FA01 1-552 ZZ000001.1 54872-55422 553-705
ZZ000002.5 1-153 BM123 1-438 ZZ000010.1 1-438 377-695 ZZ000011.1
1-320 c 411-790 ZZ000021.12 1-398 790-1191 ZZ000022.0 1-401 Entry
name FA01 TPA 1-552 ZZ000001.1 54872-55422 TPA 553-705 ZZ000002.5
1-153 Entry name BM123 TPA 1-438 ZZ000010.1 1-438 TPA 377-695
ZZ000011.1 1-320 TPA 411-790 ZZ000021.12 1-398 TPA 790-1191
ZZ000022.0 1-401 TPA Entry Name c TPA location 2014612 29 DDBJing
(DDBJ) 44
- 45. Assembly Information 1 [tab or space]TPA_SPAN[tab or
space]PRIMARY_IDENTIFIER[tab or space]PRIMARY_SPAN[tab or
space]COMPLEMENT Entry name Entry name Assembly TPA_SPAN : X..Y X-Y
(X, YX
- 46. Qualifier Copy PC Qualifier qualifier "Save" 2014612 29
DDBJing (DDBJ) 46
- 47. Edit Column paste copy paste paste "Save" 2014612 29
DDBJing (DDBJ) 47
- 48. Template: other(qualifier) (Template: other qualifier)
"Save" 2014612 29 DDBJing (DDBJ) 48
- 49. NCBI taxonomy taxonomic lineage VirusPhage taxonomy
database Organism qualifier
http://www.ddbj.nig.ac.jp/sub/ref8-j.html 2014612 29 DDBJing (DDBJ)
49 Template genetic code ( ) taxonomy database genetic code genetic
code
- 50. genetic code "7.annotation""Edit" (a) loading( ) copy &
paste loading (b) (c) genetic code TemplateCDSother genetic code
CDS /transl_table genetic code taxonomy database scientific name
genetic code genetic code genetic code The genetic
code(http://www.ddbj.nig.ac.jp/sub/geneticcode-e.html) 2014612 29
DDBJing (DDBJ) 50 (a) (b) (c)
- 51. Organism qualifier
http://www.ddbj.nig.ac.jp/sub/ref8-j.html Category Category
Category Select only for virus, environmental sample, etc.
Viruses/Phages VirusPhage VirusPhage Environmental Samples
Scientific name: uncultured Artificial Construct A known species
but unregistered in taxonomy database validNCBI taxonomy database
Not found in taxonomy database, but already registered in other
sequence data NCBI taxonomy database A novel species to be proposed
in the paper 2014612 29 DDBJing (DDBJ) 51
- 52. Category: Scientific name Organism qualifier
http://www.ddbj.nig.ac.jp/sub/ref8-j.html#species 2014612 29
DDBJing (DDBJ) 52
- 53. Category: Viruses/Phages Scientific nameVirusPhage
(Virus/Phage) Organism qualifier
http://www.ddbj.nig.ac.jp/sub/ref8-j.html#virus 2014612 29 DDBJing
(DDBJ) 53
- 54. Category: Environmental Samples Scientific name uncultured
uncultured Bacillus sp. Organism qualifier
http://www.ddbj.nig.ac.jp/sub/ref8-j.html#env 2014612 29 DDBJing
(DDBJ) 54
- 55. Category: Artificial construct Scientific name ( ) Organism
qualifier http://www.ddbj.nig.ac.jp/sub/ref8-j.html#syn 2014612 29
DDBJing (DDBJ) 55
- 56. Category: A known species but unregistered in taxonomy
database taxonomic lineage () valid () Organism qualifier database
http://www.ddbj.nig.ac.jp/sub/ref8-j.html#novel 2014612 29 DDBJing
(DDBJ) 56
- 57. Category: Not found in taxonomy database, but already
registered in other sequence data valid name () Organism qualifier
database http://www.ddbj.nig.ac.jp/sub/ref8-j.html#novel 2014612 29
DDBJing (DDBJ) 57
- 58. Category: A novel species to be proposed in the paper
taxonomic lineage () () valid name Genus sp. ##-yyyy ##yyy Organism
qualifier http://www.ddbj.nig.ac.jp/sub/ref8-j.html#unidentified
2014612 29 DDBJing (DDBJ) 58
- 59. annotation file upload DDBJ annotation file "6.Template"
annotation file other "Upload annotation file" annotation file
"Upload & Confirm" annotation file Errorannotation file Next
2014612 29 DDBJing (DDBJ) 59
- 60. Upload annotation file annotation file
(http://www.ddbj.nig.ac.jp/sub/mss/annotation_file-j.html)
annotation file () EST, STS, TSA, HTC, GSS, HTG, WGS, CON (AGP)
upload (MSS) 1. Contact person2. Hold date3. Submitter4. Reference
COMMON upload annotation file COMMON annotation file 1. Contact
person2. Hold date 3. Submitter4. Reference TPA PRIMARY_CONTIG
annotation file 5. Sequence Assembly Information annotation file
2014612 29 DDBJing (DDBJ) 60
- 61. COMMON SUBMITTER contact Hanako Mishima ab_name Mishima,H.
ab_name Yamada,T. ab_name Park,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 Japan country Japan state Shizuoka city Mishima street Yata 1111
zip 411-8540 REFERENCE ab_name Mishima,H. ab_name Yamada,T. ab_name
Park,C.S. ab_name Liu,G.Q. title Aquaporin genes year 2012 status
Unpublished DATE hold_date 20131130 ENT01 source 1..2878 organism
Homo sapiens isolate FA01 mol_type mRNA tissue_type liver CDS
217..1104 gene AQP9 product aquaporin 9 codon_start 1 transl_tabe 1
polyA_site 2878 ENT02 source 1..1409 organism Shigella flexneri
strain BM123 mol_type genomic DNA CDS