DDBJ Amino Acid Sequence Database (DAD) Release 65.0, Dec. 2013, including 29,553,914 entries, 8,770,768,717 residues Last published date in the present release: November 29, 2013 ------------------------------------------------------------------------------- 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 65.0 of DDBJ Amino Acid Sequence Database (DAD). This database has been produced by extracting all translated sequences from the DDBJ periodical release 95.0 and TPA dataset (November 2013). 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 2013, the document, DDBJ/EMBL/GenBank Feature Table: Definition, was revised in October, 2013. See also '2.9. FEATURES line' below. The revised points are introduced on the following URL; http://www.ddbj.nig.ac.jp/insdc/icm2013-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. 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 21 ddbjcon 32 ddbjenv 1 ddbjest 1 ddbjgss 1 ddbjhtc 1 ddbjhtg 1 ddbjhum 1 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 3 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 present release. In previous releases, 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 as a separate file (ddbjtpa.DAD). 9. Statistics of DAD The followings are statistics of this release of DAD. total number of entries 29,553,914 total length of sequences 8,770,768,717 aa average length 296 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 319175 96556650 1468008491 ddbjbct2.DAD 491218 149330889 1468007604 ddbjbct3.DAD 579358 178961209 1468007893 ddbjbct4.DAD 483784 153989694 1468007623 ddbjbct5.DAD 432543 137469514 1468007644 ddbjbct6.DAD 427853 134521467 1468006927 ddbjbct7.DAD 459715 142313975 1468010190 ddbjbct8.DAD 432831 134887263 1468007877 ddbjbct9.DAD 331496 107563430 1468008744 ddbjbct10.DAD 389838 121372220 1468009391 ddbjbct11.DAD 374499 119457135 1468008238 ddbjbct12.DAD 369582 116787825 1468007741 ddbjbct13.DAD 400140 127172700 1468007983 ddbjbct14.DAD 439575 138020040 1468007031 ddbjbct15.DAD 442385 138800704 1468006402 ddbjbct16.DAD 453001 141748849 1468008322 ddbjbct17.DAD 543962 171418358 1468007207 ddbjbct18.DAD 463728 142368737 1468006467 ddbjbct19.DAD 607591 178567754 1468008292 ddbjbct20.DAD 637281 195364678 1468007699 ddbjbct21.DAD 378307 103298636 784682170 ddbjcon1.DAD 205466 86182091 1468009817 ddbjcon2.DAD 270200 108709022 1468018160 ddbjcon3.DAD 206592 88397319 1468010155 ddbjcon4.DAD 314664 114873445 1468008116 ddbjcon5.DAD 329891 138795160 1468007524 ddbjcon6.DAD 451034 170510825 1468006710 ddbjcon7.DAD 447174 120950181 1468008078 ddbjcon8.DAD 366565 63950069 1468010154 ddbjcon9.DAD 366505 63915902 1468008453 ddbjcon10.DAD 366517 63913896 1468010047 ddbjcon11.DAD 366475 64024118 1468007031 ddbjcon12.DAD 366492 64037852 1468006900 ddbjcon13.DAD 366613 63961486 1468010398 ddbjcon14.DAD 367047 62756504 1468009830 ddbjcon15.DAD 364810 68931144 1468008667 ddbjcon16.DAD 361308 77088798 1468009395 ddbjcon17.DAD 363079 71819198 1468007591 ddbjcon18.DAD 360846 77144906 1468006522 ddbjcon19.DAD 363613 71132393 1468008436 ddbjcon20.DAD 358960 83103626 1468006577 ddbjcon21.DAD 358021 84670692 1468009631 ddbjcon22.DAD 356644 86682572 1468007132 ddbjcon23.DAD 357114 85622910 1468007798 ddbjcon24.DAD 453496 163797264 1468009598 ddbjcon25.DAD 443462 157393171 1468009092 ddbjcon26.DAD 388623 155685941 1468009669 ddbjcon27.DAD 419873 164364158 1468007531 ddbjcon28.DAD 366794 150270189 1468008366 ddbjcon29.DAD 365428 155153364 1468006625 ddbjcon30.DAD 413131 175859396 1468007417 ddbjcon31.DAD 430282 182466175 1468008241 ddbjcon32.DAD 140772 52845293 412569357 ddbjenv1.DAD 432247 83121531 846737092 ddbjest1.DAD 1163 153762 2555233 ddbjgss1.DAD 2859 905772 7497725 ddbjhtc1.DAD 106091 33018842 406518608 ddbjhtg1.DAD 43444 13121765 213139811 ddbjhum1.DAD 547407 161339274 1287898326 ddbjinv1.DAD 587071 168323373 1468006957 ddbjinv2.DAD 663767 176682536 1468007328 ddbjinv3.DAD 297136 69802280 657864226 ddbjmam1.DAD 204755 51560742 417714502 ddbjpat1.DAD 389523 162984947 576253207 ddbjphg1.DAD 183803 37904272 416350297 ddbjpln1.DAD 467589 162300017 1468007570 ddbjpln2.DAD 558322 166086040 1468008132 ddbjpln3.DAD 707273 195295950 1468006572 ddbjpln4.DAD 125991 33381543 265024023 ddbjpri1.DAD 66241 15630549 146060117 ddbjrod1.DAD 187263 59748469 483168762 ddbjsts1.DAD 9 812 22025 ddbjsyn1.DAD 97773 36316412 263098176 ddbjtpa1.DAD 46899 11942531 122640007 ddbjtpacon1.DAD 71398 31541167 311576389 ddbjtsa1.DAD 92052 36086038 244971068 ddbjuna1.DAD 149 23533 244245 ddbjvrl1.DAD 685235 207694873 1468006854 ddbjvrl2.DAD 682561 208017096 1468007628 ddbjvrl3.DAD 554730 176450742 1272897375 ddbjvrt1.DAD 688787 168967786 1468008024 ddbjvrt2.DAD 147023 33385276 296087041 ========================================================================= Total 29553914 8770768717 96048056274 =========================================================================