DDBJ Amino Acid Sequence Database (DAD) Release 56.0, June 2011, including 20,742,576 entries, 5,912,174,430 residues Last published date in the present release: May 27, 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 56.0 of DDBJ Amino Acid Sequence Database (DAD). This database has been produced by extracting all translated sequences from the DDBJ periodical release 86.0 and TPA dataset (June 2011). 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 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 : 12 files ddbjcon : 25 files ddbjinv : 2 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 20,742,576 total length of sequences 5,912,174,430 aa average length 285 aa name of longest sequence CP000108-608 PID:ABB27887.1 length of longest sequence 36,805 aa (CP000108-608) ========================================================================= file name number of entries number of residues file size ========================================================================= ddbjbct1.DAD 477,780 143,434,236 1,500,001,058 ddbjbct10.DAD 477,168 152,318,431 1,500,000,726 ddbjbct11.DAD 520,611 165,197,737 1,500,000,753 ddbjbct12.DAD 151,765 38,723,981 278,007,431 ddbjbct2.DAD 670,475 197,370,015 1,500,000,035 ddbjbct3.DAD 540,835 166,097,624 1,500,000,676 ddbjbct4.DAD 512,296 162,844,809 1,500,001,390 ddbjbct5.DAD 478,878 152,163,042 1,500,001,612 ddbjbct6.DAD 479,567 150,095,308 1,500,000,850 ddbjbct7.DAD 505,545 156,268,876 1,500,001,204 ddbjbct8.DAD 445,862 141,459,755 1,500,001,004 ddbjbct9.DAD 447,877 141,874,051 1,500,002,091 ddbjcon1.DAD 238,222 97,614,812 1,499,999,968 ddbjcon10.DAD 364,931 88,587,113 1,500,000,800 ddbjcon11.DAD 365,279 85,952,848 1,500,001,014 ddbjcon12.DAD 398,070 118,523,091 1,500,000,595 ddbjcon13.DAD 499,436 186,632,074 1,500,000,481 ddbjcon14.DAD 299,387 118,239,813 1,500,006,965 ddbjcon15.DAD 243,011 96,839,959 1,500,003,090 ddbjcon16.DAD 417,403 158,456,274 1,500,001,553 ddbjcon17.DAD 462,808 178,712,354 1,500,001,140 ddbjcon18.DAD 492,778 184,449,421 1,500,002,739 ddbjcon19.DAD 424,058 99,617,039 1,500,003,758 ddbjcon2.DAD 352,265 96,166,697 1,500,001,854 ddbjcon20.DAD 374,524 65,358,904 1,500,002,267 ddbjcon21.DAD 374,486 65,329,474 1,500,002,729 ddbjcon22.DAD 374,486 65,331,511 1,500,003,701 ddbjcon23.DAD 374,489 65,397,176 1,500,000,478 ddbjcon24.DAD 374,470 65,441,588 1,500,002,930 ddbjcon25.DAD 168,829 29,503,743 676,076,919 ddbjcon3.DAD 374,638 64,595,786 1,500,003,062 ddbjcon4.DAD 370,877 74,887,730 1,500,001,811 ddbjcon5.DAD 369,706 78,243,073 1,500,003,314 ddbjcon6.DAD 370,530 73,370,164 1,500,001,256 ddbjcon7.DAD 369,123 78,521,545 1,500,003,683 ddbjcon8.DAD 370,722 75,535,547 1,500,000,210 ddbjcon9.DAD 365,589 86,760,062 1,500,003,299 ddbjenv.DAD 217,081 43,028,305 405,350,039 ddbjest.DAD 1,163 153,762 2,553,096 ddbjgss.DAD 61 12,916 122,434 ddbjhtc.DAD 91,624 29,214,811 380,055,247 ddbjhtg.DAD 41,009 13,865,071 113,385,448 ddbjhum.DAD 366,521 116,579,793 916,071,772 ddbjinv1.DAD 622,625 183,027,171 1,500,001,915 ddbjinv2.DAD 603,205 150,268,676 1,331,056,224 ddbjmam.DAD 139,700 34,747,443 268,050,131 ddbjpat.DAD 387,451 162,010,719 572,960,274 ddbjphg.DAD 76,143 15,867,646 161,078,404 ddbjpln1.DAD 535,365 184,359,163 1,500,001,278 ddbjpln2.DAD 636,926 181,815,378 1,500,001,075 ddbjpln3.DAD 43,976 15,779,522 98,873,257 ddbjpri.DAD 51,814 11,401,130 105,129,949 ddbjrod.DAD 168,958 59,012,577 449,476,604 ddbjsts.DAD 9 812 17,852 ddbjsyn.DAD 72,803 28,658,992 191,094,884 ddbjtpa.DAD 45,533 21,524,383 168,454,962 ddbjtsa.DAD 16,703 6,679,080 42,480,118 ddbjuna.DAD 473 106,603 903,378 ddbjvrl1.DAD 740,949 210,834,732 1,500,001,250 ddbjvrl2.DAD 445,392 138,895,233 943,238,364 ddbjvrt.DAD 538,316 138,414,849 1,160,956,732 ========================================================================= total 20,742,576 5,912,174,430 66,765,463,133 =========================================================================