===== ===== ===== ===== ===== ===== ===== ===== ===== ===== ===== ===== THIS DATABASE MAY BE COPIED AND REDISTRIBUTED WITHOUT PERMISSION ON THE CONDITION THAT ALL THE STATEMENTS IN THIS RELEASE NOTE ARE REPRODUCED IN EACH COPY. ===== ===== ===== ===== ===== ===== ===== ===== ===== ===== ===== ===== DDBJ Amino Acid Sequence Database (DAD) Release 53.0 September 29, 2010 including 18,225,996 entries, 5,103,235,346 residues This is release 53.0 of DDBJ Amino Acid Sequence Database (DAD). This database has been produced by extracting all translated sequences from the DDBJ periodical release 83.0 and TPA dataset (September 2010). 1. DAD files 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 2. Announcement for changes in the present release Nothing particular. 3. Announcement for the forthcoming changes Revision of the DDBJ/EMBL/GenBank Feature Table: Definition: Following the agreement at the INSD collaborative meeting in 2010, the document, DDBJ/EMBL/GenBank Feature Table: Definition, will be revised in October, 2010. The revised points are introduced in advance on the following URL; http://www.ddbj.nig.ac.jp/insdc/icm2010-e.html#ft At DDBJ, the retrofit for this revision will be completed by the next DAD periodical release to be published in January 2011. Please note that during this transitional period, some entries will be retrofitted. 4. 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. 5. 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 ----- ----- ----- ----- 6. 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 '5. 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, '7. 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). 7. Statistics of DAD The following are statistics of this release of DAD. total number of entries 18,225,996 total length of sequences 5,103,235,346 aa average length 279 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 481,343 144,779,633 1,500,000,692 ddbjbct2.DAD 547,084 167,428,282 1,500,001,361 ddbjbct3.DAD 517,268 164,386,203 1,500,003,582 ddbjbct4.DAD 477,567 151,795,291 1,500,001,414 ddbjbct5.DAD 480,660 150,403,069 1,500,001,145 ddbjbct6.DAD 510,140 158,181,952 1,500,002,536 ddbjbct7.DAD 451,986 143,226,644 1,500,002,668 ddbjbct8.DAD 456,108 145,571,939 1,500,002,494 ddbjbct9.DAD 690,902 199,467,073 1,500,003,139 ddbjbct10.DAD 35,189 10,356,926 91,649,945 ddbjcon1.DAD 236,950 97,244,117 1,500,001,729 ddbjcon2.DAD 352,807 96,061,181 1,500,003,421 ddbjcon3.DAD 374,576 64,669,284 1,500,002,218 ddbjcon4.DAD 370,760 75,268,686 1,500,001,533 ddbjcon5.DAD 369,765 78,047,788 1,500,002,475 ddbjcon6.DAD 370,452 73,506,706 1,500,000,161 ddbjcon7.DAD 369,255 78,234,888 1,500,003,339 ddbjcon8.DAD 370,492 76,051,486 1,500,002,545 ddbjcon9.DAD 365,614 86,721,835 1,500,000,002 ddbjcon10.DAD 364,942 88,585,002 1,500,003,370 ddbjcon11.DAD 365,290 85,926,254 1,500,003,386 ddbjcon12.DAD 409,262 122,675,836 1,500,002,080 ddbjcon13.DAD 479,426 178,237,623 1,500,000,018 ddbjcon14.DAD 303,949 117,050,802 1,500,007,615 ddbjcon15.DAD 256,190 94,079,866 1,500,004,264 ddbjcon16.DAD 417,573 166,770,528 1,500,001,138 ddbjcon17.DAD 501,669 184,339,951 1,500,000,333 ddbjcon18.DAD 394,587 77,017,869 1,500,002,683 ddbjcon19.DAD 374,450 65,442,465 1,500,003,232 ddbjcon20.DAD 374,497 65,358,569 1,500,002,463 ddbjcon21.DAD 374,487 65,364,929 1,500,000,684 ddbjcon22.DAD 374,560 65,262,917 1,500,003,310 ddbjcon23.DAD 374,385 65,507,888 1,500,000,813 ddbjcon24.DAD 115,620 20,180,109 462,749,050 ddbjenv.DAD 168,342 33,065,323 313,206,405 ddbjest.DAD 1,163 153,762 2,553,936 ddbjgss.DAD 61 12,916 122,434 ddbjhtc.DAD 89,791 28,869,875 369,995,539 ddbjhtg.DAD 43,865 16,928,657 129,787,155 ddbjhum.DAD 334,925 107,690,220 854,218,386 ddbjinv1.DAD 635,071 183,084,323 1,500,002,817 ddbjinv2.DAD 257,012 62,049,467 576,557,651 ddbjmam.DAD 123,334 31,026,725 236,669,612 ddbjpat.DAD 375,990 157,673,790 556,790,267 ddbjphg.DAD 62,149 12,936,081 126,994,149 ddbjpln1.DAD 480,127 162,640,744 1,500,000,827 ddbjpln2.DAD 503,401 141,523,018 1,099,572,229 ddbjpri.DAD 48,491 10,519,573 98,644,969 ddbjrod.DAD 162,282 57,171,025 435,987,394 ddbjsts.DAD 9 812 17,852 ddbjsyn.DAD 66,829 26,355,670 177,509,892 ddbjtpa.DAD 44,599 21,300,583 155,168,946 ddbjtsa.DAD 4,814 1,177,824 9,345,644 ddbjuna.DAD 2,597 760,176 4,994,564 ddbjvrl1.DAD 748,585 211,138,056 1,500,001,404 ddbjvrl2.DAD 296,691 92,782,892 628,269,959 ddbjvrt.DAD 466,063 121,170,243 1,015,445,289 ========================================================================= total 18,225,996 5,103,235,346 59,846,328,158 ========================================================================= 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)