===== ===== ===== ===== ===== ===== ===== ===== ===== ===== ===== ===== 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 54.0 Junuary 14, 2011 including 18,867,995 entries, 5,305,737,486 residues This is release 54.0 of DDBJ Amino Acid Sequence Database (DAD). This database has been produced by extracting all translated sequences from the DDBJ periodical release 84.0 and TPA dataset (December 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. 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 March 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 18,867,995 total length of sequences 5,305,737,486 aa average length 281 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 480,255 144,346,438 1,500,002,155 ddbjbct2.DAD 541,017 165,842,422 1,500,001,739 ddbjbct3.DAD 524,147 166,274,817 1,500,000,844 ddbjbct4.DAD 473,484 150,670,304 1,500,000,000 ddbjbct5.DAD 481,444 150,504,828 1,500,003,755 ddbjbct6.DAD 509,801 158,265,602 1,500,002,428 ddbjbct7.DAD 457,174 144,538,888 1,500,005,038 ddbjbct8.DAD 448,924 142,705,424 1,500,002,623 ddbjbct9.DAD 606,908 181,436,124 1,500,001,772 ddbjbct10.DAD 404,615 117,824,453 892,089,488 ddbjcon1.DAD 288,173 100,841,643 1,500,001,277 ddbjcon2.DAD 371,762 128,553,726 1,500,001,560 ddbjcon3.DAD 415,772 93,028,962 1,500,003,149 ddbjcon4.DAD 388,654 85,959,897 1,500,000,079 ddbjcon5.DAD 374,434 65,412,316 1,500,002,295 ddbjcon6.DAD 365,629 65,788,540 1,500,001,110 ddbjcon7.DAD 349,149 72,340,850 1,500,002,653 ddbjcon8.DAD 374,506 65,308,034 1,500,002,237 ddbjcon9.DAD 371,487 65,078,090 1,500,003,382 ddbjcon10.DAD 375,100 64,107,320 1,500,000,164 ddbjcon11.DAD 372,670 77,559,907 1,500,003,544 ddbjcon12.DAD 369,250 78,356,637 1,500,003,010 ddbjcon13.DAD 370,766 74,424,926 1,500,003,777 ddbjcon14.DAD 368,867 78,263,200 1,500,002,702 ddbjcon15.DAD 365,667 85,368,193 1,500,000,272 ddbjcon16.DAD 363,661 90,584,152 1,500,000,792 ddbjcon17.DAD 333,610 74,023,928 1,500,002,707 ddbjcon18.DAD 367,400 83,275,384 1,500,001,106 ddbjcon19.DAD 375,142 95,448,029 1,500,001,230 ddbjcon20.DAD 334,316 135,872,285 1,500,006,318 ddbjcon21.DAD 476,196 169,621,178 1,500,001,377 ddbjcon22.DAD 352,422 130,229,358 1,500,002,646 ddbjcon23.DAD 409,148 160,975,261 1,500,001,651 ddbjcon24.DAD 265,223 103,283,926 865,886,046 ddbjenv.DAD 186,887 37,109,331 348,053,295 ddbjest.DAD 1,164 154,137 2,554,995 ddbjgss.DAD 61 12,916 122,434 ddbjhtc.DAD 89,889 28,893,711 377,318,492 ddbjhtg.DAD 45,821 17,575,037 136,056,178 ddbjhum.DAD 344,569 110,742,293 875,387,495 ddbjinv1.DAD 632,924 182,866,787 1,500,000,664 ddbjinv2.DAD 320,160 75,803,191 703,792,951 ddbjmam.DAD 126,947 31,939,119 243,390,243 ddbjpat.DAD 384,040 160,583,797 567,917,984 ddbjphg.DAD 69,077 14,469,876 148,125,095 ddbjpln1.DAD 477,347 162,451,356 1,500,000,760 ddbjpln2.DAD 554,571 155,157,228 1,194,358,716 ddbjpri.DAD 49,985 10,948,473 101,464,811 ddbjrod.DAD 164,912 57,871,305 441,708,536 ddbjsts.DAD 9 812 17,852 ddbjsyn.DAD 70,110 27,543,715 185,543,480 ddbjtpa.DAD 44,535 21,277,872 156,024,574 ddbjtsa.DAD 5108 1,232,891 9,884,007 ddbjuna.DAD 469 105,738 895,910 ddbjvrl1.DAD 746,658 210,376,700 1,500,001,006 ddbjvrl2.DAD 339,706 106,804,528 720,184,042 ddbjvrt.DAD 486,273 125,701,631 1,055,368,928 ========================================================================= total 18,867,995 5,305,737,486 61,526,217,374 ========================================================================= 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)