DDBJ Amino Acid Sequence Database (DAD) Release 61.0, Dec. 2012, including 25,302,083 entries, 7,351,129,523 residues Last published date in the present release: November 22, 2012 ------------------------------------------------------------------------------- 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 61.0 of DDBJ Amino Acid Sequence Database (DAD). This database has been produced by extracting all translated sequences from the DDBJ periodical release 91.0 and TPA dataset (December 2012). 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 2012, the document, DDBJ/EMBL/GenBank Feature Table: Definition, was revised in November, 2012. The revised points are introduced on the following URL; http://www.ddbj.nig.ac.jp/insdc/icm2012-e.html#ft Please note that during this transitional period, some entries will be retrofitted. 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 16 ddbjcon 28 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 25,302,083 total length of sequences 7,351,129,523 aa average length 290 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 471407 141269384 1468008462 ddbjbct2.DAD 512888 160366691 1468007706 ddbjbct3.DAD 556772 171440483 1468006804 ddbjbct4.DAD 472115 151710523 1468008342 ddbjbct5.DAD 464247 146607876 1468008434 ddbjbct6.DAD 470652 146474291 1468009073 ddbjbct7.DAD 508862 156204826 1468008097 ddbjbct8.DAD 397428 129384335 1468006636 ddbjbct9.DAD 452977 141369432 1468010838 ddbjbct10.DAD 474717 150404415 1468007391 ddbjbct11.DAD 488294 155858034 1468008975 ddbjbct12.DAD 542812 170699571 1468008237 ddbjbct13.DAD 575159 178491132 1468008680 ddbjbct14.DAD 635096 187688052 1468006705 ddbjbct15.DAD 706871 206811046 1468010346 ddbjbct16.DAD 34920 10273359 90289569 ddbjcon1.DAD 229920 94794821 1468008439 ddbjcon2.DAD 259561 106615681 1468009584 ddbjcon3.DAD 201496 85433525 1468008904 ddbjcon4.DAD 373501 133867344 1468008207 ddbjcon5.DAD 460482 185011949 1468010843 ddbjcon6.DAD 485110 159232766 1468009708 ddbjcon7.DAD 366510 63998252 1468009766 ddbjcon8.DAD 366467 64020571 1468007313 ddbjcon9.DAD 366537 63941852 1468007514 ddbjcon10.DAD 366500 63925896 1468006777 ddbjcon11.DAD 366544 63932652 1468009153 ddbjcon12.DAD 366449 64190828 1468008585 ddbjcon13.DAD 367196 62737656 1468009921 ddbjcon14.DAD 366018 65175969 1468006848 ddbjcon15.DAD 361500 76611090 1468008449 ddbjcon16.DAD 362513 74280151 1468007481 ddbjcon17.DAD 361671 74277813 1468010212 ddbjcon18.DAD 362470 74202462 1468006496 ddbjcon19.DAD 360915 78150928 1468009996 ddbjcon20.DAD 358190 84497098 1468008554 ddbjcon21.DAD 356763 87237181 1468007793 ddbjcon22.DAD 357533 83891152 1468009364 ddbjcon23.DAD 413820 132804634 1468009491 ddbjcon24.DAD 472721 177680601 1468006548 ddbjcon25.DAD 416393 151840208 1468007491 ddbjcon26.DAD 419825 166224807 1468007710 ddbjcon27.DAD 403308 155786480 1468007611 ddbjcon28.DAD 168817 66627628 629136595 ddbjenv1.DAD 340009 65085217 642425474 ddbjest1.DAD 1163 153762 2565862 ddbjgss1.DAD 61 12916 122495 ddbjhtc1.DAD 95830 30009285 387154334 ddbjhtg1.DAD 40282 12370462 116121078 ddbjhum1.DAD 475478 146233601 1145045794 ddbjinv1.DAD 617812 175911685 1468011220 ddbjinv2.DAD 685096 180770609 1468008126 ddbjinv3.DAD 980 464731 3378815 ddbjmam1.DAD 178882 44777167 348077288 ddbjpat1.DAD 388161 162358314 573788261 ddbjphg1.DAD 135254 27858426 295378744 ddbjpln1.DAD 530447 178514787 1468007494 ddbjpln2.DAD 553354 168346847 1468008159 ddbjpln3.DAD 571950 157752955 1135820390 ddbjpri1.DAD 60352 13679618 124281304 ddbjrod1.DAD 189840 64027650 490568095 ddbjsts1.DAD 9 812 17752 ddbjsyn1.DAD 82875 31297452 211331831 ddbjtpa1.DAD 26712 11462888 92807911 ddbjtpacon1.DAD 71668 31580322 296500012 ddbjtsa1.DAD 82607 31725238 214555997 ddbjuna1.DAD 458 103317 872317 ddbjvrl1.DAD 715428 207814294 1468008468 ddbjvrl2.DAD 677945 211397710 1468006980 ddbjvrl3.DAD 175100 53624110 376550207 ddbjvrt1.DAD 700321 172664347 1468006921 ddbjvrt2.DAD 20062 5085556 38083710 ========================================================================= Total 25302083 7351129523 79147284687 =========================================================================