===== ===== ===== ===== ===== ===== ===== ===== ===== ===== ===== ===== 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 45.0 October 14, 2008 including 13,052,722 entries, 3,443,700,325 residues This is release 45.0 of DDBJ Amino Acid Sequence Database (DAD). This database has been produced by extracting all translated sequences from the release 75.0 of the INSDC (International Nucleotide Sequence Database Collaboration, DDBJ/EMBL/GenBank) entries (September 2008). 1. DAD files DAD entries are classified into 22 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. Announcement for changes in the present release 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. 3. Announcement for the forthcoming changes Revision of the DDBJ/EMBL/GenBank Feature Table: Definition: Following the agreement at the INSD collaborative meeting in 2008, the document, DDBJ/EMBL/GenBank Feature Table: Definition, will be revised in October, 2008. The revised points are introduced in advance on the following URL; http://www.ddbj.nig.ac.jp/insdc/icm2008-e.html#ft At DDBJ, the retrofit for this revision will be completed by the next periodical release to be published in December 2008. 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 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 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 13,052,722 total length of sequences 3,443,700,325 aa average length 263 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 510,658 154,153,548 1,500,001,162 ddbjbct2.DAD 540,181 164,677,621 1,500,001,757 ddbjbct3.DAD 497,100 159,332,334 1,500,000,762 ddbjbct4.DAD 486,719 154,281,952 1,499,999,967 ddbjbct5.DAD 495,345 155,234,448 1,500,001,843 ddbjbct6.DAD 271,644 77,475,854 651,648,435 ddbjcon1.DAD 274,667 124,224,345 1,500,003,088 ddbjcon10.DAD 380,256 94,002,122 1,500,001,610 ddbjcon11.DAD 324,059 130,275,243 1,500,000,208 ddbjcon12.DAD 419,396 141,265,486 1,500,003,275 ddbjcon13.DAD 391,877 68,370,176 1,500,002,932 ddbjcon14.DAD 391,739 68,354,446 1,500,000,796 ddbjcon15.DAD 339,953 72,311,016 1,500,001,624 ddbjcon16.DAD 391,828 68,325,522 1,500,003,830 ddbjcon17.DAD 391,780 68,458,701 1,500,001,545 ddbjcon18.DAD 400,180 73,638,475 1,500,001,751 ddbjcon19.DAD 392,467 67,213,219 1,500,001,064 ddbjcon2.DAD 368,803 75,985,537 1,500,000,160 ddbjcon20.DAD 26,600 4,559,954 101,905,602 ddbjcon3.DAD 386,080 82,115,147 1,500,000,002 ddbjcon4.DAD 386,799 76,791,952 1,500,001,183 ddbjcon5.DAD 385,502 82,341,649 1,500,001,736 ddbjcon6.DAD 388,508 75,974,002 1,500,000,161 ddbjcon7.DAD 382,479 90,259,033 1,500,000,430 ddbjcon8.DAD 381,804 91,289,210 1,500,002,689 ddbjcon9.DAD 378,052 96,518,074 1,500,001,280 ddbjenv.DAD 94,349 18,706,510 173,091,682 ddbjest.DAD 1,164 153,938 2,514,126 ddbjgss.DAD 61 12,916 122,434 ddbjhtc.DAD 86,055 27,966,628 362,253,856 ddbjhtg.DAD 28,538 13,527,160 91,764,206 ddbjhum.DAD 282,701 92,587,786 747,141,719 ddbjinv.DAD 458,325 140,930,596 1,175,140,492 ddbjmam.DAD 88,066 22,636,098 169,756,293 ddbjpat.DAD 56,545 17,960,270 74,488,947 ddbjphg.DAD 42,621 8,831,948 91,540,652 ddbjpln1.DAD 434,663 150,860,520 1,500,002,546 ddbjpln2.DAD 259,281 79,364,877 581,229,252 ddbjpri.DAD 36,404 7,959,076 75,924,861 ddbjrod.DAD 143,030 52,280,089 397,666,927 ddbjsts.DAD 9 812 19,972 ddbjsyn.DAD 44,365 17,064,330 120,167,878 ddbjtpa.DAD 5,956 2,020,026 13,128,658 ddbjtsa.DAD 506 100,772 947,197 ddbjuna.DAD 463 104,263 880,441 ddbjvrl.DAD 704,522 191,168,993 1,389,203,444 ddbjvrt.DAD 300,622 82,033,651 680,966,840 ========================================================================= total 13,052,722 3,443,700,325 44,401,541,315 ========================================================================= 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)