DDBJ Amino Acid Sequence Database (DAD) Release 69.0, Dec. 2014, including 36,947,790 entries, 11,288,302,791 residues Last published date in the present release: November 25, 2014 ------------------------------------------------------------------------------- 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. Contact information 5. Disclaimer 6. DAD file categories 7. A sample of DAD entries 8. Release history 9. Statistics of DAD ------------------------------------------------------------------------------- 1. Introduction This is release 69.0 of DDBJ Amino Acid Sequence Database (DAD). This database has been produced by extracting all translated sequences from the DDBJ periodical release 99.0 and TPA dataset (November 2014). 1.1. Announcement for changes in the present release Nothing particular. 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. 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/ 5. 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. 6. 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 30 ddbjcon 37 ddbjenv 1 ddbjest 1 ddbjgss 1 ddbjhtc 1 ddbjhtg 1 ddbjhum 2 ddbjinv 3 ddbjmam 1 ddbjpat 1 ddbjphg 1 ddbjpln 4 ddbjpri 1 ddbjrod 1 ddbjsts 1 ddbjsyn 1 ddbjtpa 1 ddbjtpacon 1 ddbjtsa 1 ddbjuna 1 ddbjvrl 4 ddbjvrt 2 ------------------------------- 7. 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 ----- ----- ----- ----- 8. 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 '7. 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). 9. Statistics of DAD The followings are statistics of this release of DAD. total number of entries 36,947,790 total length of sequences 11,288,302,791 average length 305 aa 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 322859 97665116 1468006884 ddbjbct2.DAD 496112 150815548 1468031314 ddbjbct3.DAD 587477 183592554 1468007943 ddbjbct4.DAD 505307 158311188 1468007523 ddbjbct5.DAD 424856 136562986 1468008624 ddbjbct6.DAD 433573 135610380 1468007414 ddbjbct7.DAD 437534 136625371 1468007177 ddbjbct8.DAD 471228 144308984 1468008912 ddbjbct9.DAD 328852 107202060 1468011244 ddbjbct10.DAD 386289 120938230 1468009749 ddbjbct11.DAD 405860 127369354 1468010060 ddbjbct12.DAD 329945 105449614 1468009111 ddbjbct13.DAD 394394 124989438 1468010451 ddbjbct14.DAD 460132 144516038 1468006621 ddbjbct15.DAD 443321 138650088 1468010590 ddbjbct16.DAD 397852 125863840 1468008611 ddbjbct17.DAD 562639 176652508 1468008669 ddbjbct18.DAD 536831 166067094 1468009068 ddbjbct19.DAD 444675 136757216 1468009018 ddbjbct20.DAD 389010 121470197 1468006429 ddbjbct21.DAD 359095 108726254 1468012238 ddbjbct22.DAD 318415 95378690 1468009098 ddbjbct23.DAD 350389 106494054 1468010260 ddbjbct24.DAD 463545 142240136 1468007856 ddbjbct25.DAD 436403 136843766 1468008252 ddbjbct26.DAD 431263 139301404 1468007621 ddbjbct27.DAD 525332 154260784 1468006850 ddbjbct28.DAD 594331 182770582 1468006479 ddbjbct29.DAD 697831 204049389 1468008349 ddbjbct30.DAD 333083 92581816 647021292 ddbjcon1.DAD 207181 87841747 1468010531 ddbjcon2.DAD 272394 109116869 1468011626 ddbjcon3.DAD 206781 88619054 1468008687 ddbjcon4.DAD 301535 112929219 1468007992 ddbjcon5.DAD 289697 111549716 1468008491 ddbjcon6.DAD 488021 197797912 1468007074 ddbjcon7.DAD 468371 151906198 1468008863 ddbjcon8.DAD 366500 63974963 1468008778 ddbjcon9.DAD 366470 64049245 1468007615 ddbjcon10.DAD 366531 63961380 1468007125 ddbjcon11.DAD 366512 63961405 1468007699 ddbjcon12.DAD 366558 63917879 1468009952 ddbjcon13.DAD 366453 64153285 1468006763 ddbjcon14.DAD 367158 62868229 1468009449 ddbjcon15.DAD 366166 64742744 1468009934 ddbjcon16.DAD 361553 76601499 1468008776 ddbjcon17.DAD 362462 74494120 1468009847 ddbjcon18.DAD 361761 73985403 1468010004 ddbjcon19.DAD 362372 74458636 1468008240 ddbjcon20.DAD 361104 77746157 1468007033 ddbjcon21.DAD 358072 84545831 1468010776 ddbjcon22.DAD 356957 87148739 1468007928 ddbjcon23.DAD 357527 83856179 1468007015 ddbjcon24.DAD 407149 126007125 1468009301 ddbjcon25.DAD 457289 172544563 1468006892 ddbjcon26.DAD 404985 148295879 1468008434 ddbjcon27.DAD 403614 164224808 1468010182 ddbjcon28.DAD 476326 196390531 1468009055 ddbjcon29.DAD 325664 134213693 1468006686 ddbjcon30.DAD 346816 146944448 1468007181 ddbjcon31.DAD 369800 156384564 1468006864 ddbjcon32.DAD 454727 202491419 1468008732 ddbjcon33.DAD 453161 181152357 1468007105 ddbjcon34.DAD 432438 192202307 1468007059 ddbjcon35.DAD 485024 196470196 1468007562 ddbjcon36.DAD 473617 209617050 1468008197 ddbjcon37.DAD 162710 61054655 485431305 ddbjenv1.DAD 573818 114458111 1212312451 ddbjest1.DAD 1163 153762 2562668 ddbjgss1.DAD 2898 925769 7587555 ddbjhtc1.DAD 107566 33501015 410112302 ddbjhtg1.DAD 37617 11767239 196040768 ddbjhum1.DAD 619761 181179223 1468006436 ddbjhum2.DAD 34093 9891114 73831905 ddbjinv1.DAD 571132 169402532 1468007965 ddbjinv2.DAD 664074 176935089 1468006749 ddbjinv3.DAD 588724 148016027 1251015790 ddbjmam1.DAD 229748 57782230 467235638 ddbjpat1.DAD 391047 163728370 579450775 ddbjphg1.DAD 228934 46955751 516009754 ddbjpln1.DAD 464075 163661117 1468006535 ddbjpln2.DAD 547835 166341443 1468007341 ddbjpln3.DAD 700360 204326532 1468007787 ddbjpln4.DAD 430399 104289778 861572422 ddbjpri1.DAD 72333 17075521 158123122 ddbjrod1.DAD 197519 62424023 504424277 ddbjsts1.DAD 9 812 22050 ddbjsyn1.DAD 117408 43896674 313167782 ddbjtpa1.DAD 47572 12135615 125485755 ddbjtpacon1.DAD 71668 31580322 309013571 ddbjtsa1.DAD 120360 49444651 324014850 ddbjuna1.DAD 214 35721 356911 ddbjvrl1.DAD 667683 209390402 1468007711 ddbjvrl2.DAD 691677 208382552 1468006804 ddbjvrl3.DAD 632446 205075499 1468008468 ddbjvrl4.DAD 200797 70222750 459348052 ddbjvrt1.DAD 691357 169884379 1468006915 ddbjvrt2.DAD 273614 61154085 551694916 ========================================================================= Total 36947790 11288302791 119556484485 =========================================================================