===== ===== ===== ===== ===== ===== ===== ===== ===== ===== ===== ===== 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 40.0 July 23, 2007 including 10,900,421 entries, 2,729,493,910 residues This is release 40.0 of DDBJ Amino Acid Sequence Database (DAD). This database has been produced by extracting all translated sequences from the release 70.1 of the INSDC (International Nucleotide Sequence Database Collaboration, DDBJ/EMBL/GenBank) entries (June 2007). 1. DAD files DAD entries are classified into 21 categories according to the classification of the original nucleotide sequences. 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. Recent changes 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. 3. Announcement for the forthcoming changes Deletion of E-mail address, phone and fax numbers from DAD flat file To follow Japanese law protecting personal information, DDBJ will 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 plans to retorofit most of all entries submitted to DDBJ, not to GenBank or EMBL, by periodical release 42, January 2008. Now, the submitter information is 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 will be 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 will be 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 ------------------------------------------------------------------------------- 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 27-OCT-1997 DEFINITION Homo sapiens RVP1 protein. ACCESSION AB000714-1 PROTEIN_ID BAA22986.1 SOURCE Homo sapiens 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. Jun Katahira, Institute for Microbial Diseases, Osaka University, Department of Bacterial Toxinology; 3-1, Yamadaoka, Suita, Osaka 565, Japan (E-mail:katahira@biken.osaka-u.ac.jp, Tel:81-6-879-8285, Fax:81-6-879-8283) 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 /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 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 10,900,421 total length of sequences 2,729,493,910 aa average length 250 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 513,290 155,295,743 1,500,002,564 ddbjbct2.DAD 519,004 158,022,235 1,500,002,313 ddbjbct3.DAD 487,731 157,118,886 1,500,000,120 ddbjbct4.DAD 426,292 129,125,766 1,191,513,127 ddbjcon1.DAD 387,371 89,742,156 1,500,001,494 ddbjcon2.DAD 391,769 68,435,474 1,500,003,623 ddbjcon3.DAD 388,247 76,471,674 1,500,003,336 ddbjcon4.DAD 381,270 91,645,588 1,500,002,198 ddbjcon5.DAD 381,647 90,110,767 1,500,002,670 ddbjcon6.DAD 382,533 90,202,223 1,500,001,197 ddbjcon7.DAD 372,097 114,014,071 1,500,002,608 ddbjcon8.DAD 350,198 105,890,308 1,500,002,862 ddbjcon9.DAD 387,598 78,537,185 1,500,001,108 ddbjcon10.DAD 386,461 79,284,254 1,500,003,590 ddbjcon11.DAD 387,082 80,257,801 1,500,000,378 ddbjcon12.DAD 387,189 80,120,601 1,500,002,025 ddbjcon13.DAD 391,820 67,855,305 1,500,000,266 ddbjcon14.DAD 392,103 68,153,632 1,500,000,367 ddbjcon15.DAD 391,724 68,473,102 1,500,001,055 ddbjcon16.DAD 391,856 68,367,094 1,500,001,942 ddbjcon17.DAD 369,027 64,395,092 1,412,719,576 ddbjenv.DAD 57,591 11,496,587 105,693,722 ddbjest.DAD 942 84,566 1,824,344 ddbjgss.DAD 61 12,916 122,434 ddbjhtc.DAD 75,073 25,506,330 344,206,100 ddbjhtg.DAD 28,474 13,505,861 90,167,527 ddbjhum.DAD 224,733 73,239,188 589,062,493 ddbjinv.DAD 355,673 114,826,203 947,566,144 ddbjmam.DAD 70,179 17,692,352 133,099,544 ddbjpat.DAD 54,742 17,152,891 73,616,284 ddbjphg.DAD 32,784 6,846,853 74,032,960 ddbjpln1.DAD 411,397 143,546,670 1,500,000,483 ddbjpln2.DAD 169,897 57,458,467 407,978,413 ddbjpri.DAD 32,847 7,109,080 70,127,007 ddbjrod.DAD 130,884 47,895,738 355,981,050 ddbjsts.DAD 9 812 20,235 ddbjsyn.DAD 33,022 10,941,386 83,516,352 ddbjtpa.DAD 5,280 1,774,198 11,030,536 ddbjuna.DAD 47 6,535 72,216 ddbjvrl.DAD 529,659 138,282,538 1,023,289,654 ddbjvrt.DAD 220,818 60,595,782 494,897,480 ========================================================================= total 10,900,421 2,729,493,910 37,410,573,397 ========================================================================= 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)