DDBJ Amino Acid Sequence Database (DAD) Release 60.0, Sep. 2012, including 24,480,625 entries, 7,093,168,589 residues Last published date in the present release: August 24, 2012 ------------------------------------------------------------------------------- Table of contents ------------------------------------------------------------------------------- 1. Introduction 1.1. Announcement for changes in the present release 1.2. Announcement for the forthcoming changes 2. Format of DAD entries 3. DAD categories 4. Contact information 5. Disclaimer 6. DAD file categories 7. A sample of DAD entries 8. Release history 9. Statistics of DAD ------------------------------------------------------------------------------- 1. Introduction This is release 60.0 of DDBJ Amino Acid Sequence Database (DAD). This database has been produced by extracting all translated sequences from the DDBJ periodical release 90.0 and TPA dataset (September 2012). 1.1. Announcement for changes in the present release Nothing particular. 1.2. Announcement for the forthcoming changes Revision of the DDBJ/EMBL/GenBank Feature Table: Definition: Following the agreement at the INSD collaborative meeting in 2012, the document, DDBJ/EMBL/GenBank Feature Table: Definition, will be revised in October, 2012. The revised points are introduced in advance on the following URL; http://www.ddbj.nig.ac.jp/insdc/icm2012-e.html#ft At DDBJ, the retrofit for this revision will be completed by the next periodical release to be published in December 2012. Please note that during this transitional period, some entries will be retrofitted. 2. 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. 3. DAD categories DAD entries are classified into 23 categories, adding TPA and TPACON 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 4. Contact information DNA Data Bank of Japan DDBJ Center 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 WWW: http://www.ddbj.nig.ac.jp/ 5. Disclaimer While DDBJ endeavors to keep its data correct, DDBJ makes no representations or warranties of any kind about the completeness, accuracy or reliability with respect to the entries contained in the DAD periodical release. DDBJ also makes no legal liability or responsibility of merchantability or fitness for a particular purpose or that the use of the sequence data will not infringe any patent or other rights. Any receipt, reliance or use you place on such data is therefore strictly at your own risk. 6. DAD file categories This release covers 23 categories (see also '3. DAD categories'.) of organisms and others as follows: ------------------------------------------------------------------------------ ddbjbct; Category for bacteria ddbjcon; Category for CON (contigs) ddbjenv; Category for ENV (environmental samples) ddbjest; Category for EST (expressed sequence tags) ddbjgss; Category for GSS (genome survey sequences) ddbjhtc; Category for HTC (high throughput cDNA sequences) ddbjhtg; Category for HTG (high throughput genomic sequences) ddbjhum; Category for human ddbjinv; Category for invertebrates ddbjmam; Category for mammals other than primates and rodents ddbjpat; Category for patents ddbjphg; Category for phages ddbjpln; Category for plants ddbjpri; Category for primates other than human ddbjrod; Category for rodents ddbjsts; Category for STS (sequence tagged sites) ddbjsyn; Category for synthetic DNAs ddbjtpa; Category for TPA (third party annotations) ddbjtpacon; Category for CON (contigs) of TPA (third party annotations) ddbjtsa; Category for TSA (transcriptome shotgun assemblies) ddbjuna; Category for unannotated sequences ddbjvrl; Category for viruses ddbjvrt; Category for vertebrates other than mammals ------------------------------------------------------------------------------ All of above in the present release are recorded in ddbj***##.DAD files as follows, respectively. file prefix number of files ------------------------------- ddbjbct 15 ddbjcon 28 ddbjenv 1 ddbjest 1 ddbjgss 1 ddbjhtc 1 ddbjhtg 1 ddbjhum 1 ddbjinv 2 ddbjmam 1 ddbjpat 1 ddbjphg 1 ddbjpln 3 ddbjpri 1 ddbjrod 1 ddbjsts 1 ddbjsyn 1 ddbjtpa 1 ddbjtpacon 1 ddbjtsa 1 ddbjuna 1 ddbjvrl 3 ddbjvrt 1 ------------------------------- 7. 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 ----- ----- ----- ----- 8. 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 '7. 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, '9. 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). 9. Statistics of DAD The followings are statistics of this release of DAD. total number of entries 24,480,625 total length of sequences 7,093,168,589 aa average length 289 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 471299 141202184 1468007346 ddbjbct2.DAD 512324 160110428 1468007266 ddbjbct3.DAD 553531 170459459 1468007828 ddbjbct4.DAD 473581 152919949 1468008068 ddbjbct5.DAD 461319 145163466 1468008143 ddbjbct6.DAD 474867 147852052 1468009071 ddbjbct7.DAD 506284 155355467 1468008706 ddbjbct8.DAD 404166 131610883 1468007278 ddbjbct9.DAD 452059 141320904 1468007169 ddbjbct10.DAD 473356 150254644 1468009653 ddbjbct11.DAD 489189 155800431 1468008126 ddbjbct12.DAD 543841 171164430 1468008081 ddbjbct13.DAD 572772 178085613 1468007597 ddbjbct14.DAD 672198 197694589 1468007775 ddbjbct15.DAD 324498 88222631 665845294 ddbjcon1.DAD 229912 94792689 1468009441 ddbjcon2.DAD 259123 106489656 1468007359 ddbjcon3.DAD 201687 85510288 1468009526 ddbjcon4.DAD 389888 145332193 1468007080 ddbjcon5.DAD 456156 179492679 1468008948 ddbjcon6.DAD 472889 147131759 1468007308 ddbjcon7.DAD 366561 63920790 1468008059 ddbjcon8.DAD 366484 63924877 1468008008 ddbjcon9.DAD 366463 63969527 1468008446 ddbjcon10.DAD 366464 64057499 1468009600 ddbjcon11.DAD 366553 63950541 1468009971 ddbjcon12.DAD 366533 64039628 1468008295 ddbjcon13.DAD 367198 62776984 1468008150 ddbjcon14.DAD 365608 66481542 1468007632 ddbjcon15.DAD 361412 76478380 1468008187 ddbjcon16.DAD 362681 73629830 1468006611 ddbjcon17.DAD 361291 75545339 1468010221 ddbjcon18.DAD 362950 72891134 1468008699 ddbjcon19.DAD 360215 79835806 1468010210 ddbjcon20.DAD 358168 84560023 1468008658 ddbjcon21.DAD 356610 87268023 1468007666 ddbjcon22.DAD 357555 83890308 1468007483 ddbjcon23.DAD 430543 143924035 1468008471 ddbjcon24.DAD 468187 173916955 1468008841 ddbjcon25.DAD 411884 153420420 1468008824 ddbjcon26.DAD 420726 168231701 1468006618 ddbjcon27.DAD 385121 144500749 1468007374 ddbjcon28.DAD 36613 14752116 139228589 ddbjenv1.DAD 324720 61925513 610756557 ddbjest1.DAD 1163 153762 2561267 ddbjgss1.DAD 61 12916 122495 ddbjhtc1.DAD 95582 29968863 386730721 ddbjhtg1.DAD 40282 12370462 116212786 ddbjhum1.DAD 470889 145055971 1131664578 ddbjinv1.DAD 616974 175462375 1468006460 ddbjinv2.DAD 635900 169400991 1370924146 ddbjmam1.DAD 174774 43765163 340022708 ddbjpat1.DAD 388161 162358314 573725252 ddbjphg1.DAD 121409 25062452 269052883 ddbjpln1.DAD 526066 177569349 1468007270 ddbjpln2.DAD 553746 167336532 1468008011 ddbjpln3.DAD 508130 139374352 1010236488 ddbjpri1.DAD 59709 13529565 123089977 ddbjrod1.DAD 187364 63549347 486242349 ddbjsts1.DAD 9 812 17752 ddbjsyn1.DAD 82113 31058035 210033005 ddbjtpa1.DAD 26631 11432988 92318478 ddbjtpacon1.DAD 42563 21807435 173939465 ddbjtsa1.DAD 82230 31655423 213808526 ddbjuna1.DAD 458 103317 872226 ddbjvrl1.DAD 717252 207698325 1468008435 ddbjvrl2.DAD 676866 211698890 1468006964 ddbjvrl3.DAD 109156 30394823 223683189 ddbjvrt1.DAD 677658 168490013 1425452170 ========================================================================= Total 24480625 7093168589 77094915834 =========================================================================