DDBJ Amino Acid Sequence Database (DAD) Release 73.0, Dec. 2015, including 45,660,142 entries, 14,219,638,761 residues Last published date in the present release: November 27, 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 73.0 of DDBJ Amino Acid Sequence Database (DAD). This database has been produced by extracting all translated sequences from the DDBJ periodical release 103.0 and TPA dataset (November 2015). 1.1. Announcement for changes in the present release 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, was revised. The revised points are introduced in advance on the following URL; http://www.ddbj.nig.ac.jp/insdc/icm2015-e.html#ft 1.2. Announcement for the forthcoming changes Nothing particular. 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 41 ddbjcon 41 ddbjenv 2 ddbjest 1 ddbjgss 1 ddbjhtc 1 ddbjhtg 1 ddbjhum 2 ddbjinv 4 ddbjmam 1 ddbjpat 1 ddbjphg 1 ddbjpln 6 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 45,660,142 total length of sequences 14,219,638,761 average length 311 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 323274 97993056 1468007327 ddbjbct2.DAD 500778 152007163 1468043085 ddbjbct3.DAD 578891 183195512 1468006612 ddbjbct4.DAD 564039 170569089 1468006947 ddbjbct5.DAD 447561 143439431 1468009742 ddbjbct6.DAD 437287 138584580 1468008037 ddbjbct7.DAD 430896 134167544 1468008801 ddbjbct8.DAD 460243 142549332 1468007086 ddbjbct9.DAD 373680 118472407 1468008140 ddbjbct10.DAD 359554 114260474 1468010151 ddbjbct11.DAD 393789 122657855 1468009628 ddbjbct12.DAD 349017 111160888 1468007135 ddbjbct13.DAD 395769 126650760 1468009288 ddbjbct14.DAD 425719 134584980 1468010438 ddbjbct15.DAD 451696 141912081 1468006638 ddbjbct16.DAD 438459 137027362 1468007123 ddbjbct17.DAD 483283 151106730 1468007270 ddbjbct18.DAD 537492 170116650 1468006583 ddbjbct19.DAD 464154 142852859 1468007179 ddbjbct20.DAD 463325 142230662 1468009084 ddbjbct21.DAD 387006 120062359 1468008181 ddbjbct22.DAD 370432 113152967 1468006769 ddbjbct23.DAD 319269 95406460 1468007563 ddbjbct24.DAD 339157 103365992 1468008879 ddbjbct25.DAD 431471 131500682 1468009774 ddbjbct26.DAD 462120 144838691 1468008900 ddbjbct27.DAD 423686 134212478 1468007022 ddbjbct28.DAD 453261 142501436 1468010213 ddbjbct29.DAD 451150 140561716 1468009369 ddbjbct30.DAD 443167 136545061 1468006787 ddbjbct31.DAD 421547 129975629 1468007835 ddbjbct32.DAD 421026 130546921 1468009820 ddbjbct33.DAD 430670 135262472 1468007413 ddbjbct34.DAD 400501 126350739 1468006698 ddbjbct35.DAD 412169 129393577 1468007643 ddbjbct36.DAD 396050 123412595 1468007979 ddbjbct37.DAD 503369 153292287 1468006617 ddbjbct38.DAD 619933 187608905 1468006584 ddbjbct39.DAD 702082 208366598 1468006566 ddbjbct40.DAD 778520 219383163 1468008198 ddbjbct41.DAD 25343 7434638 57169252 ddbjcon1.DAD 211876 92872311 1468007222 ddbjcon2.DAD 277429 115376700 1468009459 ddbjcon3.DAD 180442 95163730 1468010518 ddbjcon4.DAD 277564 113823468 1468006404 ddbjcon5.DAD 320434 118540569 1468006639 ddbjcon6.DAD 324066 138865254 1468006723 ddbjcon7.DAD 512201 208797243 1468007177 ddbjcon8.DAD 465169 176621656 1468008817 ddbjcon9.DAD 410968 95625777 1468010071 ddbjcon10.DAD 366548 63965962 1468009303 ddbjcon11.DAD 366486 63980747 1468010306 ddbjcon12.DAD 366534 63927873 1468007343 ddbjcon13.DAD 366552 63909901 1468007401 ddbjcon14.DAD 366454 64034815 1468006547 ddbjcon15.DAD 366634 63977820 1468006811 ddbjcon16.DAD 366895 62867002 1468009138 ddbjcon17.DAD 363744 71499177 1468009737 ddbjcon18.DAD 361658 76848942 1468010003 ddbjcon19.DAD 362870 71596162 1468007344 ddbjcon20.DAD 360800 77484963 1468006731 ddbjcon21.DAD 363881 71194103 1468007230 ddbjcon22.DAD 358049 84597342 1468009565 ddbjcon23.DAD 357866 84634903 1468008297 ddbjcon24.DAD 356794 86666015 1468006656 ddbjcon25.DAD 356437 87266841 1468007682 ddbjcon26.DAD 459126 177235593 1468007556 ddbjcon27.DAD 442970 156691135 1468006936 ddbjcon28.DAD 384207 157681506 1468006538 ddbjcon29.DAD 417948 164727608 1468008553 ddbjcon30.DAD 436664 181564492 1468008685 ddbjcon31.DAD 311922 132828456 1468007266 ddbjcon32.DAD 383034 164676949 1468007896 ddbjcon33.DAD 418353 180183581 1468011533 ddbjcon34.DAD 428493 184322914 1468009720 ddbjcon35.DAD 451947 185653818 1468007321 ddbjcon36.DAD 422461 185051146 1468008326 ddbjcon37.DAD 498163 201085048 1468006664 ddbjcon38.DAD 425936 181709266 1468007071 ddbjcon39.DAD 345416 115267306 1468009646 ddbjcon40.DAD 421297 192792446 1468009390 ddbjcon41.DAD 463990 190998241 1424736969 ddbjenv1.DAD 685413 138169427 1468006453 ddbjenv2.DAD 20721 4202772 42476536 ddbjest1.DAD 1163 153762 2566057 ddbjgss1.DAD 3137 962078 8032143 ddbjhtc1.DAD 112466 34132450 419035292 ddbjhtg1.DAD 64006 17465440 259504906 ddbjhum1.DAD 620295 181033523 1468006652 ddbjhum2.DAD 71261 17827850 146671434 ddbjinv1.DAD 584687 176105898 1468007623 ddbjinv2.DAD 693149 179749085 1468008393 ddbjinv3.DAD 693405 149542836 1468006907 ddbjinv4.DAD 309054 82307155 713821657 ddbjmam1.DAD 257936 65054484 526008958 ddbjpat1.DAD 391189 163810258 580947599 ddbjphg1.DAD 327072 68562677 706132073 ddbjpln1.DAD 456117 161258007 1468006440 ddbjpln2.DAD 469196 188560962 1468009629 ddbjpln3.DAD 545710 224284856 1468007356 ddbjpln4.DAD 705097 201761101 1468007940 ddbjpln5.DAD 739768 173268728 1468006658 ddbjpln6.DAD 31654 12013753 79229400 ddbjpri1.DAD 78976 18773690 172195013 ddbjrod1.DAD 211359 66081292 532734358 ddbjsts1.DAD 9 812 22053 ddbjsyn1.DAD 125975 47273283 339618379 ddbjtpa1.DAD 62967 25279119 192893726 ddbjtpacon1.DAD 71628 31568870 308879820 ddbjtsa1.DAD 121260 49590475 325766916 ddbjuna1.DAD 222 37953 376656 ddbjvrl1.DAD 661149 209405929 1468007617 ddbjvrl2.DAD 691674 207712375 1468006535 ddbjvrl3.DAD 633418 202829081 1468008222 ddbjvrl4.DAD 559479 206566301 1343083979 ddbjvrt1.DAD 693319 170518266 1468006777 ddbjvrt2.DAD 395098 88450651 794432456 ========================================================================= Total 45660142 14219638761 146969120163 =========================================================================