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  1. 1. DDBJ Nucleotide Sequence Submission System Takehide Kosuge, Ph.D DDBJ DDBJ, Annotator 2014612 29 DDBJing (DDBJ) 1
  2. 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 Reference Unpublished 38 In press 39 Published 40 JournalJournal 41 : Journal of biological chemistry 42 TPA 43 TPA Assembly Information 44 Assembly Information 45 Qualifier 46 Edit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. 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. 4. (email) (email DDBJ (annotator) DDBJ (Submitter(s)) 2014612 29 DDBJing (DDBJ) 4
  5. 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. 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. 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. 8. () http://www.ddbj.nig.ac.jp/sub/example-j.html () DDBJ 2014612 29 DDBJing (DDBJ) 8
  9. 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. 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. 11. http://www.ddbj.nig.ac.jp/ DDBJ" " 2014612 29 DDBJing (DDBJ) 11
  12. 12. DDBJ Nucleotide Sequence Submission System 2014612 29 DDBJing (DDBJ) 12
  13. 13. Web "" 2014612 29 DDBJing (DDBJ) 13
  14. 14. DDBJ Nucleotide Sequence Submission System Create new submission Firefox Chrome SafariIE10IE11 IE8 2014612 29 DDBJing (DDBJ) 14
  15. 15. Submission System 1. Contact person 2. Hold date "Create new submission" 2014612 29 DDBJing (DDBJ) 15
  16. 16. 3. Submitter 4. Reference 2014612 29 DDBJing (DDBJ) 16
  17. 17. 5. TPAAssembly Information 6. upload 2014612 29 DDBJing (DDBJ) 17
  18. 18. 7. upload 8. 2014612 29 DDBJing (DDBJ) 18
  19. 19. 2014612 29 DDBJing (DDBJ) 19
  20. 20. : 2014612 29 DDBJing (DDBJ) 20
  21. 21. 1. Contact person Email, Fax, Phone Ne DDBJ full name faxphone FAX FAX ( ) () URL() () 2014612 29 DDBJing (DDBJ) 21
  22. 22. Subject: DDBJ: Starting the submission To: [email protected] 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 [email protected] 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. 23. 2. Hold date (Hold date) 6 DDBJ 3 Ne 2014612 29 DDBJing (DDBJ) 23
  24. 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. 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. 26. 5. Sequence upload Yes "YES" "No." TPA ( TPA ) Ne URL URL 7.Annotation 2014612 29 DDBJing (DDBJ) 26
  27. 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. 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. 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. 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. 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. 32. 8. Finish DDBJ () DDBJ DDBJ DDBJ URL 2014612 29 DDBJing (DDBJ) 32
  33. 33. Contact person : [email protected] 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: [email protected] 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: [email protected] Subject: DDBJ: Web submission completed 2014612 29 DDBJing (DDBJ) 33
  34. 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. 35. 2014612 29 DDBJing (DDBJ) 35
  36. 36. "Next" "5.Sequence" "6.Template" 2014612 29 DDBJing (DDBJ) 36
  37. 37. 2. Submitter "Add" Add 2014612 29 DDBJing (DDBJ) 37
  38. 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. 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. 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. 41. JournalJournal Journal Namefull name ISO Abbreviation NLM Catalog ISO Abbreviation NLM Catalog 2014612 29 DDBJing (DDBJ) 41
  42. 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. 43. TPA upload "No" TPA TPA( ) Assembly Information upload URL URL Next 2014612 29 DDBJing (DDBJ) 43
  44. 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. 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. 46. Qualifier Copy PC Qualifier qualifier "Save" 2014612 29 DDBJing (DDBJ) 46
  47. 47. Edit Column paste copy paste paste "Save" 2014612 29 DDBJing (DDBJ) 47
  48. 48. Template: other(qualifier) (Template: other qualifier) "Save" 2014612 29 DDBJing (DDBJ) 48
  49. 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. 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. 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. 52. Category: Scientific name Organism qualifier http://www.ddbj.nig.ac.jp/sub/ref8-j.html#species 2014612 29 DDBJing (DDBJ) 52
  53. 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. 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. 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. 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. 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. 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. 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. 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. 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 [email protected] 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

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