DDBJ Amino Acid Sequence Database (DAD) Release 58.0, Dec. 2011, including 22,451,011 entries, 6,457,504,280 residues Last published date in the present release: November 25, 2011 ------------------------------------------------------------------------------- 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 58.0 of DDBJ Amino Acid Sequence Database (DAD). This database has been produced by extracting all translated sequences from the DDBJ periodical release 88.0 and TPA dataset (December 2011). 1.1. Announcement for changes in the present release Nothing particular. 1.2. Announcement for the forthcoming changes DDBJ will postpone making up DAD periodical release 59 from March to June: Since DDBJ is planning to improve its systems substantially, during the first quarter in 2012, DDBJ will skip to make up the next periodical release of DAD in March 2012. So, DAD periodical release 59 will be prepared in June 2012. 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 22 categories, adding TPA 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 Center for Information Biology and DNA Data Bank of Japan 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 (for general inquiry) WWW: http://www.ddbj.nig.ac.jp/ (for DDBJ WWW server) 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 22 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) ddbjtsa; Category for TSA (transcriptome shotgun assemblies) ddbjuna; Category for unannotated sequences ddbjvrl; Category for viruses ddbjvrt; Category for vertebrates other than mammals ------------------------------------------------------------------------------ Some of above in the present release are recorded in multiple ddbj***##.DAD files as follows, respectively. --------------------- ddbjbct : 13 files ddbjcon : 26 files ddbjinv : 3 files ddbjpln : 3 files ddbjvrl : 2 files --------------------- 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 22,451,011 total length of sequences 6,457,504,280 aa average length 287 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 480,097 144,045,525 1,500,002,293 ddbjbct10.DAD 450,587 142,459,237 1,500,000,449 ddbjbct11.DAD 476,323 151,186,089 1,500,003,579 ddbjbct12.DAD 494,002 157,232,345 1,500,000,563 ddbjbct13.DAD 256,437 80,361,828 680,969,493 ddbjbct2.DAD 657,309 194,458,829 1,500,001,507 ddbjbct3.DAD 674,687 199,031,165 1,500,001,427 ddbjbct4.DAD 534,956 164,428,453 1,500,001,973 ddbjbct5.DAD 505,871 161,163,092 1,500,002,626 ddbjbct6.DAD 480,593 152,520,102 1,500,002,788 ddbjbct7.DAD 476,576 149,325,539 1,500,001,939 ddbjbct8.DAD 501,333 154,892,908 1,500,000,107 ddbjbct9.DAD 441,727 140,407,225 1,500,000,475 ddbjcon1.DAD 309,091 116,149,303 1,500,001,577 ddbjcon10.DAD 371,429 65,007,716 1,500,002,435 ddbjcon11.DAD 375,105 64,163,208 1,500,003,247 ddbjcon12.DAD 372,869 77,169,726 1,500,000,248 ddbjcon13.DAD 368,034 81,302,915 1,500,001,605 ddbjcon14.DAD 365,302 86,033,742 1,500,002,741 ddbjcon15.DAD 366,270 85,236,208 1,500,001,691 ddbjcon16.DAD 370,969 73,369,764 1,500,002,266 ddbjcon17.DAD 368,676 78,918,472 1,500,000,786 ddbjcon18.DAD 333,638 73,954,226 1,500,003,158 ddbjcon19.DAD 367,354 83,412,286 1,500,002,714 ddbjcon2.DAD 414,672 151,878,724 1,500,007,251 ddbjcon20.DAD 368,614 92,645,105 1,500,000,510 ddbjcon21.DAD 389,115 146,604,617 1,500,002,301 ddbjcon22.DAD 331,838 133,717,407 1,500,001,793 ddbjcon23.DAD 479,423 164,538,917 1,500,001,275 ddbjcon24.DAD 325,660 128,658,671 1,500,001,253 ddbjcon25.DAD 433,480 169,275,000 1,500,001,325 ddbjcon26.DAD 183,203 77,214,942 598,694,402 ddbjcon3.DAD 388,910 148,174,832 1,500,001,026 ddbjcon4.DAD 423,656 99,999,057 1,500,000,485 ddbjcon5.DAD 385,361 81,942,464 1,500,002,927 ddbjcon6.DAD 374,415 65,389,414 1,500,002,196 ddbjcon7.DAD 372,057 65,567,180 1,500,000,279 ddbjcon8.DAD 342,732 72,602,690 1,500,002,860 ddbjcon9.DAD 374,520 65,325,022 1,500,002,523 ddbjenv.DAD 259,609 51,070,841 484,625,187 ddbjest.DAD 1,163 153,762 2,543,442 ddbjgss.DAD 61 12,916 122,495 ddbjhtc.DAD 92,593 29,394,713 381,653,097 ddbjhtg.DAD 46,532 15,300,841 133,232,555 ddbjhum.DAD 380,046 119,398,257 940,701,578 ddbjinv1.DAD 628,047 186,289,558 1,500,002,259 ddbjinv2.DAD 699,606 167,035,302 1,500,001,708 ddbjinv3.DAD 44,977 14,719,145 111,893,348 ddbjmam.DAD 156,290 39,084,295 302,983,566 ddbjpat.DAD 387,720 162,156,183 573,510,804 ddbjphg.DAD 100,877 20,817,036 218,908,436 ddbjpln1.DAD 537,964 184,525,210 1,500,003,248 ddbjpln2.DAD 579,872 179,456,538 1,500,000,870 ddbjpln3.DAD 236,770 62,787,628 453,830,474 ddbjpri.DAD 57,691 13,059,183 119,210,574 ddbjrod.DAD 175,341 60,490,469 461,300,581 ddbjsts.DAD 9 812 17,798 ddbjsyn.DAD 79,502 30,109,850 204,539,462 ddbjtpa.DAD 67,120 32,638,745 260,610,062 ddbjtsa.DAD 25,279 8,849,662 59,586,725 ddbjuna.DAD 458 103,264 867,286 ddbjvrl1.DAD 738,881 212,592,037 1,500,000,396 ddbjvrl2.DAD 577,210 178,107,179 1,242,663,533 ddbjvrt.DAD 590,502 149,586,909 1,263,737,145 ========================================================================= total 22,451,011 6,457,504,280 71,496,280,722 =========================================================================