===== ===== ===== ===== ===== ===== ===== ===== ===== ===== ===== ===== 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 51.0 April 9, 2010 including 16,673,634 entries, 4,623,895,321 residues This is release 51.0 of DDBJ Amino Acid Sequence Database (DAD). This database has been produced by extracting all translated sequences from the release 81.0 of the INSDC (International Nucleotide Sequence Database Collaboration, DDBJ/EMBL/GenBank) entries (March 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/database/ddbj/ddbjrel.txt 2. Announcement for changes in the present release Nothing particular. 3. Announcement for the forthcoming changes DDBJ will postpone making up DAD periodical release 53 from October to January: Since DDBJ is planning to improve its systems substantially, during the third quarter in 2010, DDBJ will skip to make up DDBJ periodical release after the next in September 2010. Accordingly, DAD release will be skipped at the same schedule with DDBJ release. DAD periodical release 53 will be prepared in January 2011. 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 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 16,673,634 total length of sequences 4,623,895,321 aa average length 277 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 480,460 144,309,988 1,500,001,829 ddbjbct2.DAD 547,506 167,684,099 1,500,000,565 ddbjbct3.DAD 515,797 163,955,888 1,500,000,604 ddbjbct4.DAD 480,937 152,848,529 1,500,000,475 ddbjbct5.DAD 481,751 150,735,093 1,500,002,240 ddbjbct6.DAD 512,837 158,590,180 1,500,000,325 ddbjbct7.DAD 465,302 149,447,511 1,500,001,337 ddbjbct8.DAD 620,223 179,303,762 1,465,018,173 ddbjcon1.DAD 279,470 90,045,042 1,500,002,894 ddbjcon10.DAD 372,141 73,871,457 1,500,001,227 ddbjcon11.DAD 370,824 75,019,909 1,500,000,757 ddbjcon12.DAD 369,733 78,187,809 1,500,003,780 ddbjcon13.DAD 370,439 73,375,784 1,500,003,884 ddbjcon14.DAD 360,015 79,044,624 1,500,002,575 ddbjcon15.DAD 341,011 76,396,609 1,500,001,798 ddbjcon16.DAD 364,932 87,247,842 1,500,000,068 ddbjcon17.DAD 365,233 87,637,186 1,500,002,559 ddbjcon18.DAD 365,798 86,500,033 1,500,002,603 ddbjcon19.DAD 362,288 130,381,154 1,500,004,938 ddbjcon2.DAD 449,824 127,402,241 1,500,002,208 ddbjcon20.DAD 426,445 157,666,980 1,499,999,967 ddbjcon21.DAD 370,445 142,898,476 1,499,999,950 ddbjcon22.DAD 390,409 154,177,341 1,500,005,897 ddbjcon23.DAD 101,288 39,764,244 553,608,007 ddbjcon3.DAD 374,558 65,318,821 1,500,002,513 ddbjcon4.DAD 387,688 85,973,747 1,500,002,352 ddbjcon5.DAD 374,516 65,360,888 1,500,002,174 ddbjcon6.DAD 340,321 72,707,556 1,500,001,774 ddbjcon7.DAD 374,576 65,249,125 1,500,002,291 ddbjcon8.DAD 372,985 65,230,997 1,499,999,996 ddbjcon9.DAD 374,951 64,885,965 1,500,003,438 ddbjenv.DAD 145,259 28,382,018 267,323,852 ddbjest.DAD 1,164 153,938 2,555,623 ddbjgss.DAD 61 12,916 122,434 ddbjhtc.DAD 88,817 28,614,578 368,231,522 ddbjhtg.DAD 32,688 13,895,875 104,296,253 ddbjhum.DAD 317,613 103,040,067 821,359,031 ddbjinv1.DAD 635,383 181,876,012 1,500,000,612 ddbjinv2.DAD 31,900 13,121,283 109,820,860 ddbjmam.DAD 112,172 28,524,114 215,945,288 ddbjpat.DAD 298,747 125,915,345 443,247,031 ddbjphg.DAD 57,170 11,899,665 117,353,994 ddbjpln1.DAD 480,449 162,571,801 1,500,000,986 ddbjpln2.DAD 442,437 128,850,742 987,023,734 ddbjpri.DAD 45,697 9,805,860 93,534,896 ddbjrod.DAD 155,303 56,006,910 422,649,476 ddbjsts.DAD 9 812 17,852 ddbjsyn.DAD 64,886 25,667,949 172,660,319 ddbjtpa.DAD 23,046 10,309,505 72,262,948 ddbjtsa.DAD 1,956 348,854 3,509,793 ddbjuna.DAD 469 105,738 895,748 ddbjvrl1.DAD 753,606 210,433,298 1,500,001,159 ddbjvrl2.DAD 195,836 61,543,042 417,377,021 ddbjvrt.DAD 42,4263 111,596,119 927,799,051 ========================================================================= total 16,673,634 4,623,895,321 55,566,672,681 ========================================================================= 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)