DDBJ Amino Acid Sequence Database (DAD) Release 70.0, Mar. 2015, including 39,229,464 entries, 12,028,089,596 residues Last published date in the present release: February 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. 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 70.0 of DDBJ Amino Acid Sequence Database (DAD). This database has been produced by extracting all translated sequences from the DDBJ periodical release 100.0 and TPA dataset (February 2015). 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 32 ddbjcon 39 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 39,229,464 total length of sequences 12,028,089,596 average length 306 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 323585 97995036 1468006765 ddbjbct2.DAD 497850 151247193 1468025064 ddbjbct3.DAD 580719 183206608 1468007337 ddbjbct4.DAD 520906 161437622 1468009356 ddbjbct5.DAD 428287 137302360 1468009384 ddbjbct6.DAD 435308 136457368 1468010463 ddbjbct7.DAD 437009 136158355 1468009126 ddbjbct8.DAD 482333 147528207 1468008431 ddbjbct9.DAD 326663 106304029 1468008823 ddbjbct10.DAD 385051 120792536 1468006890 ddbjbct11.DAD 398696 125496857 1468007819 ddbjbct12.DAD 343875 109282494 1468009012 ddbjbct13.DAD 379395 121012837 1468011442 ddbjbct14.DAD 461375 145225960 1468007134 ddbjbct15.DAD 452655 141416144 1468006756 ddbjbct16.DAD 388170 123045816 1468010881 ddbjbct17.DAD 548356 171161033 1468008996 ddbjbct18.DAD 558918 174071957 1468006586 ddbjbct19.DAD 444166 136402802 1468007132 ddbjbct20.DAD 435354 134140417 1468009373 ddbjbct21.DAD 358612 109760936 1468007310 ddbjbct22.DAD 320621 96698652 1468008431 ddbjbct23.DAD 325667 97692900 1468009267 ddbjbct24.DAD 422540 129676907 1468007151 ddbjbct25.DAD 454386 143308377 1468006920 ddbjbct26.DAD 425432 133837187 1468008367 ddbjbct27.DAD 443560 137222963 1468006423 ddbjbct28.DAD 480717 145424490 1468008952 ddbjbct29.DAD 437842 134345845 1468006454 ddbjbct30.DAD 625011 184644643 1468007074 ddbjbct31.DAD 650842 197266243 1468006931 ddbjbct32.DAD 684620 189594376 1340695119 ddbjcon1.DAD 217226 93452340 1468011933 ddbjcon2.DAD 275992 109020777 1468007263 ddbjcon3.DAD 194131 85423629 1468010278 ddbjcon4.DAD 295119 106966277 1468007893 ddbjcon5.DAD 287696 112462330 1468007871 ddbjcon6.DAD 493153 205459040 1468007758 ddbjcon7.DAD 475303 171646162 1468007538 ddbjcon8.DAD 370036 65960846 1468009655 ddbjcon9.DAD 366515 64011488 1468006498 ddbjcon10.DAD 366537 63959796 1468007528 ddbjcon11.DAD 366479 63943280 1468007040 ddbjcon12.DAD 366581 63901393 1468006940 ddbjcon13.DAD 366417 64058248 1468008286 ddbjcon14.DAD 366938 63562573 1468008003 ddbjcon15.DAD 366473 63412214 1468009913 ddbjcon16.DAD 362527 74677526 1468010145 ddbjcon17.DAD 361980 76090867 1468006607 ddbjcon18.DAD 362484 72114417 1468009988 ddbjcon19.DAD 361390 76588894 1468006761 ddbjcon20.DAD 362764 74098113 1468009583 ddbjcon21.DAD 357798 84910210 1468006666 ddbjcon22.DAD 357143 86672089 1468010520 ddbjcon23.DAD 357560 84165835 1468010298 ddbjcon24.DAD 374636 102850335 1468009354 ddbjcon25.DAD 486482 182027644 1468007940 ddbjcon26.DAD 408293 147904860 1468011502 ddbjcon27.DAD 388203 160994405 1468009148 ddbjcon28.DAD 483123 195155731 1468006569 ddbjcon29.DAD 346249 142867078 1468007986 ddbjcon30.DAD 327540 138398587 1468010812 ddbjcon31.DAD 378770 159568180 1468006469 ddbjcon32.DAD 432742 184511860 1468006572 ddbjcon33.DAD 469664 199725426 1468009415 ddbjcon34.DAD 398961 181678383 1468007052 ddbjcon35.DAD 506854 202923551 1468007668 ddbjcon36.DAD 462340 200085669 1468007325 ddbjcon37.DAD 368751 131441003 1468008985 ddbjcon38.DAD 404078 163295399 1468007137 ddbjcon39.DAD 212224 85008621 603587837 ddbjenv1.DAD 602672 119738402 1270564460 ddbjest1.DAD 1163 153762 2543742 ddbjgss1.DAD 2898 925769 7587555 ddbjhtc1.DAD 108032 33653827 410648841 ddbjhtg1.DAD 37661 11781675 196295335 ddbjhum1.DAD 620599 181367637 1468007174 ddbjhum2.DAD 42552 11859368 91224056 ddbjinv1.DAD 576533 170096025 1468006621 ddbjinv2.DAD 693988 180373842 1468007451 ddbjinv3.DAD 621210 152503046 1310067212 ddbjmam1.DAD 234775 58997588 476771396 ddbjpat1.DAD 391080 163745794 579518244 ddbjphg1.DAD 240708 49414370 540320661 ddbjpln1.DAD 464481 163464668 1468006868 ddbjpln2.DAD 540707 170703710 1468007209 ddbjpln3.DAD 702755 202359440 1468006731 ddbjpln4.DAD 502401 120757274 1007188776 ddbjpri1.DAD 73929 17509318 161799610 ddbjrod1.DAD 202326 63617176 513658311 ddbjsts1.DAD 9 812 21973 ddbjsyn1.DAD 118764 44403748 316210878 ddbjtpa1.DAD 47621 12151718 126503023 ddbjtpacon1.DAD 71628 31568870 308879820 ddbjtsa1.DAD 120372 49450798 324036829 ddbjuna1.DAD 214 35721 355720 ddbjvrl1.DAD 667380 209588927 1468007461 ddbjvrl2.DAD 692341 208533613 1468008271 ddbjvrl3.DAD 632478 204987198 1468006755 ddbjvrl4.DAD 258392 92294000 593671434 ddbjvrt1.DAD 693182 170303952 1468008462 ddbjvrt2.DAD 300940 67593322 604445370 ========================================================================= Total 39229464 12028089596 126759258154 =========================================================================