===== ===== ===== ===== ===== ===== ===== ===== ===== ===== ===== ===== 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 41.0 October 11, 2007 including 11,364,503 entries, 2,882,657,043 residues This is release 41.0 of DDBJ Amino Acid Sequence Database (DAD). This database has been produced by extracting all translated sequences from the release 71.0 of the INSDC (International Nucleotide Sequence Database Collaboration, DDBJ/EMBL/GenBank) entries (September 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 Nothing particular. 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 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 11,364,503 total length of sequences 2,882,657,043 aa average length 254 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 513,020 155,267,939 1,500,000,696 ddbjbct2.DAD 519,841 158,002,969 1,500,003,648 ddbjbct3.DAD 492,756 159,194,700 1,500,001,237 ddbjbct4.DAD 506,277 157,330,257 1,499,999,961 ddbjbct5.DAD 98,859 27,485,642 233,586,828 ddbjcon1.DAD 448,359 135,883,152 1,500,003,373 ddbjcon10.DAD 391,854 68,317,606 1,500,002,725 ddbjcon11.DAD 396,428 97,587,288 1,500,000,620 ddbjcon12.DAD 391,781 68,416,863 1,500,001,829 ddbjcon13.DAD 391,830 68,419,068 1,500,002,675 ddbjcon14.DAD 393,441 76,135,231 1,500,003,521 ddbjcon15.DAD 391,934 67,614,093 1,500,002,563 ddbjcon16.DAD 387,540 79,162,928 1,500,002,793 ddbjcon17.DAD 386,890 80,833,462 1,500,001,499 ddbjcon18.DAD 155,338 29,351,064 599,382,403 ddbjcon2.DAD 387,160 79,671,926 1,500,003,836 ddbjcon3.DAD 385,130 83,741,812 1,500,001,585 ddbjcon4.DAD 382,508 90,234,780 1,500,002,108 ddbjcon5.DAD 380,799 92,861,656 1,500,001,739 ddbjcon6.DAD 384,446 92,976,684 1,500,001,124 ddbjcon7.DAD 341,528 92,246,775 1,500,002,656 ddbjcon8.DAD 311,987 80,055,602 1,500,001,543 ddbjcon9.DAD 391,760 68,471,688 1,500,001,527 ddbjenv.DAD 62,506 12,309,454 114,530,094 ddbjest.DAD 1,164 153,938 2,416,906 ddbjgss.DAD 61 12,916 122,434 ddbjhtc.DAD 77,163 25,796,869 347,824,939 ddbjhtg.DAD 28,473 13,506,232 90,561,773 ddbjhum.DAD 237,096 76,863,412 619,709,355 ddbjinv.DAD 372,887 118,839,711 980,411,793 ddbjmam.DAD 75,599 19,547,014 146,413,207 ddbjpat.DAD 55,608 17,437,619 74,845,983 ddbjphg.DAD 34,281 7,171,066 76,644,069 ddbjpln1.DAD 419,923 145,289,924 1,500,001,849 ddbjpln2.DAD 175,087 58,998,599 425,153,217 ddbjpri.DAD 33,520 7,282,470 71,390,306 ddbjrod.DAD 132,998 48,514,954 362,623,917 ddbjsts.DAD 9 812 20,235 ddbjsyn.DAD 34,434 11,533,695 88,413,745 ddbjtpa.DAD 5,500 1,863,968 11,549,538 ddbjuna.DAD 458 102,881 868,323 ddbjvrl.DAD 555,022 144,723,426 1,072,848,327 ddbjvrt.DAD 231,248 63,444,898 518,077,746 ========================================================================= total 11,364,503 2,882,657,043 38,837,440,245 ========================================================================= 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)