DDBJ Amino Acid Sequence Database (DAD) Release 62.0, Mar. 2013, including 26,351,045 entries, 7,698,263,093 residues Last published date in the present release: February 22, 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 62.0 of DDBJ Amino Acid Sequence Database (DAD). This database has been produced by extracting all translated sequences from the DDBJ periodical release 92.0 and TPA dataset (February 2013). 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 19 ddbjcon 29 ddbjenv 1 ddbjest 1 ddbjgss 1 ddbjhtc 1 ddbjhtg 1 ddbjhum 1 ddbjinv 3 ddbjmam 1 ddbjpat 1 ddbjphg 1 ddbjpln 3 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 26,351,045 total length of sequences 7,698,263,093 aa average length 292 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 325469 98710231 1468009996 ddbjbct2.DAD 504382 153953117 1468008055 ddbjbct3.DAD 564956 174727570 1468007697 ddbjbct4.DAD 470828 150217245 1468006661 ddbjbct5.DAD 442554 140273224 1468008434 ddbjbct6.DAD 427023 133388459 1468007623 ddbjbct7.DAD 471653 145960359 1468006858 ddbjbct8.DAD 403743 127092222 1468011163 ddbjbct9.DAD 337518 109178597 1468006908 ddbjbct10.DAD 385846 120380936 1468010460 ddbjbct11.DAD 377236 119410165 1468006749 ddbjbct12.DAD 379916 120815859 1468012213 ddbjbct13.DAD 419648 132634214 1468006748 ddbjbct14.DAD 446559 140583412 1468007866 ddbjbct15.DAD 417676 130916040 1468011030 ddbjbct16.DAD 510961 160145587 1468011019 ddbjbct17.DAD 637246 188161138 1468008243 ddbjbct18.DAD 694266 201724494 1468007729 ddbjbct19.DAD 31870 9376112 71495931 ddbjcon1.DAD 203179 85447563 1468009750 ddbjcon2.DAD 272531 109253987 1468006497 ddbjcon3.DAD 194600 83296950 1468006802 ddbjcon4.DAD 315570 115107175 1468011017 ddbjcon5.DAD 451035 178743859 1468008969 ddbjcon6.DAD 469977 174749094 1468007164 ddbjcon7.DAD 376707 69808389 1468008143 ddbjcon8.DAD 366483 64047027 1468006653 ddbjcon9.DAD 366509 63958610 1468010323 ddbjcon10.DAD 366481 63995591 1468008158 ddbjcon11.DAD 366597 63881087 1468007056 ddbjcon12.DAD 366467 63983652 1468006547 ddbjcon13.DAD 366854 63651555 1468006929 ddbjcon14.DAD 366528 63337894 1468008491 ddbjcon15.DAD 362703 74123755 1468008768 ddbjcon16.DAD 361885 76378446 1468009457 ddbjcon17.DAD 362618 71794226 1468008235 ddbjcon18.DAD 361133 77115440 1468007253 ddbjcon19.DAD 363142 73206339 1468008751 ddbjcon20.DAD 357823 84754076 1468007063 ddbjcon21.DAD 357064 86894733 1468007044 ddbjcon22.DAD 357645 84090423 1468006649 ddbjcon23.DAD 366777 98625871 1468008994 ddbjcon24.DAD 488930 185483183 1468008877 ddbjcon25.DAD 427161 152528180 1468009865 ddbjcon26.DAD 375049 155539244 1468006478 ddbjcon27.DAD 408620 156183653 1468007309 ddbjcon28.DAD 311596 119549330 1468008939 ddbjcon29.DAD 302472 130382843 1162003008 ddbjenv1.DAD 356491 68430135 702569293 ddbjest1.DAD 1163 153762 2565160 ddbjgss1.DAD 61 12916 122495 ddbjhtc1.DAD 96404 30121648 388575517 ddbjhtg1.DAD 40378 12415120 197192974 ddbjhum1.DAD 479679 142369821 1145890243 ddbjinv1.DAD 587753 167379775 1468006860 ddbjinv2.DAD 661827 175818890 1468007617 ddbjinv3.DAD 133261 33958132 312345080 ddbjmam1.DAD 184981 46467724 376695844 ddbjpat1.DAD 388341 162465461 574208581 ddbjphg1.DAD 142954 29438208 312082975 ddbjpln1.DAD 481266 166717712 1468007531 ddbjpln2.DAD 562079 166068510 1468007637 ddbjpln3.DAD 655325 182910222 1341736908 ddbjpri1.DAD 60938 13864105 134452249 ddbjrod1.DAD 177668 57018799 462168851 ddbjsts1.DAD 9 812 22075 ddbjsyn1.DAD 90623 33675594 231713029 ddbjtpa1.DAD 26716 11465212 93636450 ddbjtpacon1.DAD 71668 31580322 309016007 ddbjtsa1.DAD 85727 32578620 223018676 ddbjuna1.DAD 139 21843 226854 ddbjvrl1.DAD 709825 207730467 1468008267 ddbjvrl2.DAD 675823 209979383 1468006965 ddbjvrl3.DAD 278397 88696474 621391837 ddbjvrt1.DAD 695609 169535908 1468006422 ddbjvrt2.DAD 42454 9826362 82230079 ========================================================================= Total 26351045 7698263093 86549793048 =========================================================================