DDBJ Amino Acid Sequence Database (DAD) Release 72.0, Sep. 2015, including 43,653,463 entries, 13,562,515,245 residues Last published date in the present release: August 28, 2015 ------------------------------------------------------------------------------- Table of contents ------------------------------------------------------------------------------- 1. Introduction 1.1. Announcement for changes in the present release 1.2. Announcement for the forthcoming changes 2. Format of DAD entries 3. DAD categories 4. Citation 5. Contact information 6. Disclaimer 7. DAD file categories 8. A sample of DAD entries 9. Release history 10. Statistics of DAD ------------------------------------------------------------------------------- 1. Introduction This is release 72.0 of DDBJ Amino Acid Sequence Database (DAD). This database has been produced by extracting all translated sequences from the DDBJ periodical release 102.0 and TPA dataset (August 2015). 1.1. Announcement for changes in the present release Nothing particular. 1.2. Announcement for the forthcoming changes Revision of the DDBJ/EMBL/GenBank Feature Table: Definition: Following the agreement at the INSD collaborative meeting in 2015, the document, DDBJ/EMBL/GenBank Feature Table: Definition, will be revisedin near future. See also '2.9. FEATURES line' below. The revised points are introduced in advance on the following URL; http://www.ddbj.nig.ac.jp/insdc/icm2015-e.html#ft At DDBJ, the retrofit for this revision will be completed by the next periodical release to be published in December 2015. 2. Format of DAD entries The standard format of DAD is almost the same as that of the DDBJ nucleotide sequence database except for those described below. Accession numbers of the DAD entries are written in the lines labeled as "ACCESSION." An accession number of DAD is comprised of a DDBJ accession number and an integer that begins with 1. These two numbers are combined by a hyphen (-). For example, two amino acid sequences extracted from a DDBJ entry D12345 respectively have accession numbers of D12345-1 and D12345-2. The number is useful for identifying a DAD entry. An amino acid sequence begins from the next line of "BEGIN." Up to sixty amino acids are written in one line. Following the amino acid sequence, there is a double slash (//) which means the end of the entry. LOCUS line contains locus name, length of protein, molecular type (this is always "PRT"), division name, and date of release of DNA counterpart. DEFINITION line contains species name and protein name. The other parts of a DAD entry, including FEATURES, are almost the same as those of the corresponding DDBJ entry. 3. DAD categories DAD entries are classified into 23 categories, adding TPA and TPACON to the 21 categories of DDBJ periodical release. Please refer to the release note of the DDBJ release for details (filename: ddbjrel.txt). Also, there are two types of DAD files for each division; files with suffix ".DAD" in the DAD standard format, and those with suffix ".DAD.fasta" in a FASTA-compatible format. [DDBJ release note] ftp://ftp.ddbj.nig.ac.jp/ddbj_database/ddbj/ddbjrel.txt 4. Citation When you use DAD in your research, we would appreciate it if you would include a reference to DDBJ in your publications related to your research. When citing an entry in the DAD database, it is appropriate to give the protein_id and its accession number. Also, it is recommended to cite the first publication in REFERENCE of the entry other than submitter information. DDBJ suggests authors add a reference to DDBJ itself. The following publication, which describes the recent activities of the DDBJ center, would be appropriate to be cited: Kodama Y, Mashima J, Kosuge T, Katayama T, Fujisawa T, Kaminuma E, Ogasawara O, Okubo K, Takagi T, and Nakamura Y. The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data. Nucleic Acids Res. 43 (Database issue), D18-D22 (2015) DOI: 10.1093/nar/gku1120 The following sentence is an example to cite an entry in the DAD database: ----------------------------------------------------------------------------- "We searched the DAD database (1) by sequence similarities and found an amino acid sequence (2), with protein_id BAA22986.1 in DDBJ accession number AB000714, which had significant similarity with ..." (1) Kodama, Y. et al, Nucleic Acids Res. 43(Database issue), D18-D22 (2015). (2) Katahira, J. et al, J. Biol. Chem. 272, 26652-26658 (1997). ------------------------------------------------------------------------------ 5. Contact information DNA Data Bank of Japan DDBJ Center National Institute of Genetics Research Organization of Information and Systems Mishima 411-8540, Japan Phone: +81 55 981 6853 FAX: +81 55 981 6849 E-mail: ddbj@ddbj.nig.ac.jp WWW: http://www.ddbj.nig.ac.jp/ 6. Disclaimer While DDBJ endeavors to keep its data correct, DDBJ makes no representations or warranties of any kind about the completeness, accuracy or reliability with respect to the entries contained in the DAD periodical release. DDBJ also makes no legal liability or responsibility of merchantability or fitness for a particular purpose or that the use of the sequence data will not infringe any patent or other rights. Any receipt, reliance or use you place on such data is therefore strictly at your own risk. 7. DAD file categories This release covers 23 categories (see also '3. DAD categories'.) of organisms and others as follows: ------------------------------------------------------------------------------ ddbjbct; Category for bacteria ddbjcon; Category for CON (contigs) ddbjenv; Category for ENV (environmental samples) ddbjest; Category for EST (expressed sequence tags) ddbjgss; Category for GSS (genome survey sequences) ddbjhtc; Category for HTC (high throughput cDNA sequences) ddbjhtg; Category for HTG (high throughput genomic sequences) ddbjhum; Category for human ddbjinv; Category for invertebrates ddbjmam; Category for mammals other than primates and rodents ddbjpat; Category for patents ddbjphg; Category for phages ddbjpln; Category for plants ddbjpri; Category for primates other than human ddbjrod; Category for rodents ddbjsts; Category for STS (sequence tagged sites) ddbjsyn; Category for synthetic DNAs ddbjtpa; Category for TPA (third party annotations) ddbjtpacon; Category for CON (contigs) of TPA (third party annotations) ddbjtsa; Category for TSA (transcriptome shotgun assemblies) ddbjuna; Category for unannotated sequences ddbjvrl; Category for viruses ddbjvrt; Category for vertebrates other than mammals ------------------------------------------------------------------------------ All of above in the present release are recorded in ddbj***##.DAD files as follows, respectively. file prefix number of files ------------------------------- ddbjbct 38 ddbjcon 41 ddbjenv 1 ddbjest 1 ddbjgss 1 ddbjhtc 1 ddbjhtg 1 ddbjhum 2 ddbjinv 4 ddbjmam 1 ddbjpat 1 ddbjphg 1 ddbjpln 5 ddbjpri 1 ddbjrod 1 ddbjsts 1 ddbjsyn 1 ddbjtpa 1 ddbjtpacon 1 ddbjtsa 1 ddbjuna 1 ddbjvrl 4 ddbjvrt 2 ------------------------------- 8. A sample of DAD entries Below is a typical DAD entry. This might be useful for understanding its format and contents. ----- ----- ----- ----- sample begin ----- ----- ----- ----- LOCUS BAA22986.1 220 aa PRT HUM 28-OCT-1997 DEFINITION Homo sapiens RVP1 protein. ACCESSION AB000714-1 PROTEIN_ID BAA22986.1 SOURCE Homo sapiens (human) ORGANISM Homo sapiens Eukaryotae; Metazoa; Chordata; Vertebrata; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 1250) AUTHORS Katahira,J. TITLE Direct Submission JOURNAL Submitted (26-JAN-1997) to the DDBJ/EMBL/GenBank databases. Contact:Jun Katahira Institute for Microbial Diseases, Osaka University, Department of Bacterial Toxinology; 3-1, Yamadaoka, Suita, Osaka 565, Japan REFERENCE 2 AUTHORS Katahira,J., Sugiyama,H., Inoue,N., Horiguchi,Y., Matsuda,M. and Sugimoto,N. TITLE Clostridium perfringens enterotoxin utilizes two structurally related membrane proteins as functional receptors in vivo JOURNAL J. Biol. Chem. 272, 26652-26658 (1997) COMMENT FEATURES Qualifiers source /db_xref="H-InvDB:HIT000057926" /mol_type="mRNA" /organism="Homo sapiens" /tissue_lib="lung" protein /gene="hRVP1" /transl_table=1 BEGIN 1 MSMGLEITGT ALAVLGWLGT IVCCALPMWR VSAFIGSNII TSQNIWEGLW MNCVVQSTGQ 61 MQCKVYDSLL ALPQDLQAAR ALIVVAILLA AFGLLVALVG AQCTNCVQDD TAKAKITIVA 121 GVLFLLAALL TLVPVSWSAN TIIRDFYNPV VPEAQKREMG AGLYVGWAAA ALQLLGGALL 181 CCSCPPREKK YTATKVVYSA PRSTGPGASL GTGYDRKDYV // ----- ----- ----- ----- sample end ----- ----- ----- ----- 9. Release history ------------------ Since release 50 ------------------ The format of the SOURCE line in DAD flat file has been changed: As results of this change, 1) the order of organism name and organelle name is changed and 2) some of DAD flat files have included a common name like as GenBank flat files. The change is shown below in detail. ---------------- Old (-rel. 49) ---------------- Format: SOURCE [] Example: SOURCE Homo sapiens mitochondrion ---------------- New (rel. 50-) ---------------- Format: SOURCE [] [()] Example: SOURCE mitochondrion Homo sapiens (human) See also '8. A sample of DAD entries'. ------------------ Since release 45 ------------------ A new division, TSA (Transcriptome Shotgun Assembly) is started: A new division for assembled mRNA sequences, Transcriptome Shotgun Assembly (TSA), is included in the present release. With new sequencing technologies, INSDC has faced many requests to accept assembled EST sequences. These sequence data have become more useful than used to be, although they may not be correctly assembled or exist in nature. Therefore, INSDC decided to collect assembled EST sequences into the new division 'TSA'. TSA sequences are shotgun assemblies of primary sequences deposited in the EST division of INSDC, the Trace Archive (TA) or the Short-Read Archive (SRA). Two specific keywords, "TSA" and "Transcriptome Shotgun Assembly", are present in all TSA entries. The new division code, "TSA", is also described in the LOCUS line in all TSA entries. No format changes are anticipated for this new division, however, note that TSA entries make use of the same PRIMARY line that is described for the entries in TPA category. The PRIMARY block contains references to the underlying reads/transcripts that were assembled to construct a TSA record. ------------------ Since release 42 ------------------ Deletion of E-mail address, phone and fax numbers from DAD flat file To follow the Japanese law of protecting personal information, DDBJ delete both phone and fax numbers, and E-mail address from the flat files of entries submitted to DDBJ. Also, it would be helpful to protect DAD releases against SPAM mail senders. DDBJ retrofitted most of all entries submitted to DDBJ, not to GenBank or EMBL, by the DDBJ periodical release 72. Before the DAD periodical release 42, the submitter information was described in JOURNAL line at REFERENCE 1 as, ------------------------------------------------------------------------------- REFERENCE 1 (bases 1 to 1200) AUTHORS Mishima,T. TITLE Direct Submission JOURNAL Submitted (01-Jan-1990) to the DDBJ/EMBL/GenBank databases. Taro Mishima, DNA Data Bank of Japan, National Institute of Genetics; 1111, Yata, Mishima, Shizuoka 411-8540, Japan (E-mail:ddbj@ddbj.nig.ac.jp, URL:http://www.ddbj.nig.ac.jp/, Tel:81-12-345-6789, Fax:81-12-345-9876) ------------------------------------------------------------------------------- After the deletion or the information in question, DAD flat file is either one of the following two types; Type 1: Phone and fax numbers and E-mail address are deleted. ------------------------------------------------------------------------------- REFERENCE 1 (bases 1 to 1200) AUTHORS Mishima,T. TITLE Direct Submission JOURNAL Submitted (01-Jan-1990) to the DDBJ/EMBL/GenBank databases. Contact:Taro Mishima DNA Data Bank of Japan, National Institute of Genetics; 1111, Yata, Mishima, Shizuoka 411-8540, Japan URL :http://www.ddbj.nig.ac.jp/ ------------------------------------------------------------------------------- Type 2: When the submitters wish to keep their contact information disclosed, it is described as, ------------------------------------------------------------------------------- REFERENCE 1 (bases 1 to 1200) AUTHORS Mishima,T. TITLE Direct Submission JOURNAL Submitted (01-Jan-1990) to the DDBJ/EMBL/GenBank databases. Contact:Taro Mishima DNA Data Bank of Japan, National Institute of Genetics; 1111, Yata, Mishima, Shizuoka 411-8540, Japan URL :http://www.ddbj.nig.ac.jp/ E-mail :ddbj@ddbj.nig.ac.jp Phone :81-12-345-6789 Fax :81-12-345-9876 ------------------------------------------------------------------------------- ------------------ Since release 40 ------------------ The CON division has been included. CON; Contig / Constructed To conjugate a series of entries, such as those submitted from a genome project, each of the three data banks constructs an entry and assign an accession number to a large scale sequence dataset. Such entries are classified into the CON division. ------------------ Since release 38 ------------------ From the present release, we change the maximum file size to 1.5 GB, because the network capacity has been remarkably increased. Each file named as ddbj***##.DAD has at most 1.5 GB storage capacity. See also the sections, '9. Statistics of DAD'. ------------------ Since release 32 ------------------ Introduction of ENV division : Recently, the submissions of the sequences derived from environmental samples have rapidly increased. To accommodate such submissions, a new division, ENV, has been created. This division contains the sequences obtained via direct molecular isolation such as PCR, DGGE, or any anonymous method. In the past, the sequences derived from environmental samples belonged to taxonomic divisions, mainly BCT. At DDBJ, the retrofit to transfer relevant entries from taxonomic divisions to the ENV division starts in the present release, and ends by the next periodical release. Please note that during this transitional period, some entries to be eventually placed in the ENV division will be found in other divisions. ------------------ Since release 30 ------------------ "H-InvDB" has been added to db_xref(cross-reference) as a qualifier key. The following is an example. FEATURES Location/Qualifiers source 1..5589 /clone="hf00223s1" /clone_lib="pBluescriptII SK plus" /db_xref="H-InvDB:HIT000000001" ------------------ Since release 29 ------------------ The GSS division has been included since release 29. GSS stands for the Genome Survey Sequence, which is similar to EST, except that GSS is genomic DNA whereas EST is cDNA. ------------------ Since release 21 ------------------ 1) Some information on introns has been added. It is given as "intron_pos" in the Feature/Qualifiers. Examples: intron_pos 142:1 (2/12) means that the 2nd intron among 12 in total is located between the 1st and 2nd bases of the 142th codon (amino acid residue). intron_pos 228:0 (4/12) means that the 4th intron among 12 in total is located between the 227th and 228th codons (between the 3rd base of the 227th codon and the 1st base of the 228th codon). 2) the Locus line has been changed. The following is an example and its explanation: LOCUS BAA21794.1 263 aa PRT BCT 05-FEB-1999 Positions Contents --------- -------- 01-05 'LOCUS' 06-12 spaces 13-28 Locus name 29-29 space 30-40 Length of sequence, right-justified 41-41 space 42-43 'aa' 44-47 spaces 48-53 'PRT' 54-64 spaces 65-67 Division code 68-68 space 69-79 Date, in the form DD-MMM-YYYY (e.g., 15-MAR-1991) --------------------- 3) TPA data have been provided in a separate file (ddbjtpa.DAD). 10. Statistics of DAD The followings are statistics of this release of DAD. total number of entries 43,653,463 total length of sequences 13,562,515,245 average length 310 name of longest sequence CP000108-608 PID:ABB27887.1 length of longest sequence 36,805 aa (CP000108-608) ========================================================================= file name no. of entries no. of amino acids file size ========================================================================= ddbjbct1.DAD 322892 97764546 1468008095 ddbjbct2.DAD 499683 151704185 1468043966 ddbjbct3.DAD 580659 183971953 1468006770 ddbjbct4.DAD 551181 167631090 1468009881 ddbjbct5.DAD 445021 142828319 1468007663 ddbjbct6.DAD 428936 134650921 1468009240 ddbjbct7.DAD 428859 134017276 1468006804 ddbjbct8.DAD 472654 144687992 1468006939 ddbjbct9.DAD 353312 113609538 1468006464 ddbjbct10.DAD 367397 115699800 1468008922 ddbjbct11.DAD 399487 125710676 1468007925 ddbjbct12.DAD 348215 110617653 1468007070 ddbjbct13.DAD 382702 122498029 1468006495 ddbjbct14.DAD 447392 140963401 1468007041 ddbjbct15.DAD 441738 139070980 1468009123 ddbjbct16.DAD 425877 133349165 1468006845 ddbjbct17.DAD 502193 156419343 1468007600 ddbjbct18.DAD 554610 175163000 1468007263 ddbjbct19.DAD 450285 138287969 1468008023 ddbjbct20.DAD 476631 146249764 1468006846 ddbjbct21.DAD 386202 119921442 1468007374 ddbjbct22.DAD 343114 104578792 1468008203 ddbjbct23.DAD 317585 95123658 1468006476 ddbjbct24.DAD 363560 110781868 1468008415 ddbjbct25.DAD 442917 135303939 1468006514 ddbjbct26.DAD 453271 143412903 1468009067 ddbjbct27.DAD 436670 138503354 1468007032 ddbjbct28.DAD 433236 135749130 1468007157 ddbjbct29.DAD 467619 143596992 1468009846 ddbjbct30.DAD 427008 131831490 1468010267 ddbjbct31.DAD 423135 129926905 1468007825 ddbjbct32.DAD 424594 133597631 1468007662 ddbjbct33.DAD 399227 124601669 1468007243 ddbjbct34.DAD 418130 131488770 1468010370 ddbjbct35.DAD 604222 177410701 1468007372 ddbjbct36.DAD 641425 196057131 1468006716 ddbjbct37.DAD 726466 198276993 1468008365 ddbjbct38.DAD 343470 106100430 639339570 ddbjcon1.DAD 213391 91362915 1468015975 ddbjcon2.DAD 278911 111697411 1468006937 ddbjcon3.DAD 193807 85311926 1468006883 ddbjcon4.DAD 294438 106616559 1468007587 ddbjcon5.DAD 275719 109520805 1468007321 ddbjcon6.DAD 492242 211078516 1468008813 ddbjcon7.DAD 455967 176356914 1468010406 ddbjcon8.DAD 456295 129380508 1468007393 ddbjcon9.DAD 366526 63990474 1468009016 ddbjcon10.DAD 366495 63969449 1468008114 ddbjcon11.DAD 366538 63953574 1468006579 ddbjcon12.DAD 366518 63953457 1468008720 ddbjcon13.DAD 366524 63946375 1468009731 ddbjcon14.DAD 366523 64058711 1468008688 ddbjcon15.DAD 367123 62738886 1468007050 ddbjcon16.DAD 364993 68348575 1468010369 ddbjcon17.DAD 361408 76791532 1468009982 ddbjcon18.DAD 363030 72141834 1468007593 ddbjcon19.DAD 360902 76918803 1468007174 ddbjcon20.DAD 363444 71480637 1468009399 ddbjcon21.DAD 359367 82108575 1468009896 ddbjcon22.DAD 358094 84608870 1468010331 ddbjcon23.DAD 356598 86942353 1468006910 ddbjcon24.DAD 357303 84850594 1468006795 ddbjcon25.DAD 443102 149546508 1468007761 ddbjcon26.DAD 438837 166430172 1468006632 ddbjcon27.DAD 399001 158447177 1468007058 ddbjcon28.DAD 384362 155235605 1468007447 ddbjcon29.DAD 482759 194390750 1468007307 ddbjcon30.DAD 311656 134794129 1468010510 ddbjcon31.DAD 357135 151887891 1468008170 ddbjcon32.DAD 408198 173313341 1468008067 ddbjcon33.DAD 425396 188376299 1468010052 ddbjcon34.DAD 450839 180854481 1468008209 ddbjcon35.DAD 435437 192075222 1468007376 ddbjcon36.DAD 481083 195216100 1468008247 ddbjcon37.DAD 475592 210837150 1468009761 ddbjcon38.DAD 332661 108564190 1468009499 ddbjcon39.DAD 411737 172997293 1468007889 ddbjcon40.DAD 455835 192595659 1468006694 ddbjcon41.DAD 47359 20152608 149541943 ddbjenv1.DAD 677443 135433588 1437381506 ddbjest1.DAD 1163 153762 2561617 ddbjgss1.DAD 2942 943098 7665367 ddbjhtc1.DAD 111893 33979635 418001711 ddbjhtg1.DAD 63998 17463810 257044196 ddbjhum1.DAD 620238 181081839 1468008123 ddbjhum2.DAD 65384 16239153 135080978 ddbjinv1.DAD 576214 170329449 1468006503 ddbjinv2.DAD 692629 179599715 1468007738 ddbjinv3.DAD 695581 152071719 1468007223 ddbjinv4.DAD 59730 29431519 131404163 ddbjmam1.DAD 248027 62428114 505350948 ddbjpat1.DAD 391127 163775977 579643879 ddbjphg1.DAD 302733 63691204 655907925 ddbjpln1.DAD 462587 163051163 1468009748 ddbjpln2.DAD 459799 194558053 1468008266 ddbjpln3.DAD 577274 216154023 1468006538 ddbjpln4.DAD 699239 202420701 1468008195 ddbjpln5.DAD 635215 153033888 1276290552 ddbjpri1.DAD 77599 18312558 169303694 ddbjrod1.DAD 206797 64655323 523045417 ddbjsts1.DAD 9 812 22053 ddbjsyn1.DAD 124526 46818638 336970066 ddbjtpa1.DAD 62847 25246902 190193194 ddbjtpacon1.DAD 71628 31568870 308879820 ddbjtsa1.DAD 120372 49450798 324031123 ddbjuna1.DAD 214 35721 360400 ddbjvrl1.DAD 661727 209136524 1468006469 ddbjvrl2.DAD 691344 207835753 1468006793 ddbjvrl3.DAD 633513 202801855 1468007165 ddbjvrl4.DAD 460817 170538716 1102482018 ddbjvrt1.DAD 693330 170531978 1468006684 ddbjvrt2.DAD 360804 80738161 725688857 ========================================================================= Total 43653463 13562515245 140528943662 =========================================================================