DDBJ Amino Acid Sequence Database (DAD) Release 55.0, Mar. 2011, including 19,723,681 entries, 5,576,482,211 residues Last published date in the present release: February 25, 2011 ------------------------------------------------------------------------------- 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 55.0 of DDBJ Amino Acid Sequence Database (DAD). This database has been produced by extracting all translated sequences from the DDBJ periodical release 85.0 and TPA dataset (March 2011). 1.1. Announcement for changes in the present release The style of release note (this file) has been changed. 1.2. Announcement for the forthcoming changes Nothing particular. 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 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 4. Contact information 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) 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 22 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) ddbjtsa; Category for TSA (transcriptome shotgun assemblies) ddbjuna; Category for unannotated sequences ddbjvrl; Category for viruses ddbjvrt; Category for vertebrates other than mammals ------------------------------------------------------------------------------ Some of above in the present release are recorded in multiple ddbj***##.DAD files as follows, respectively. --------------------- ddbjbct : 11 files ddbjcon : 24 files ddbjinv : 2 files ddbjpln : 2 files ddbjvrl : 2 files --------------------- 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 19,723,681 total length of sequences 5,576,482,211 aa average length 282 aa name of longest sequence CP000108-608 PID:ABB27887.1 length of longest sequence 36,805 aa (CP000108-608) ========================================================================= file name number of entries number of residues file size ========================================================================= ddbjbct1.DAD 477,424 143,434,214 1,500,003,162 ddbjbct2.DAD 565,168 168,131,626 1,500,001,095 ddbjbct3.DAD 556,194 173,005,410 1,500,000,340 ddbjbct4.DAD 472,221 151,202,750 1,500,000,241 ddbjbct5.DAD 483,942 151,419,112 1,500,004,526 ddbjbct6.DAD 502,343 156,363,118 1,500,000,352 ddbjbct7.DAD 493,036 153,198,876 1,500,003,044 ddbjbct8.DAD 431,108 137,804,996 1,500,002,007 ddbjbct9.DAD 483,656 154,584,460 1,500,001,986 ddbjbct10.DAD 616,132 183,102,992 1,500,000,742 ddbjbct11.DAD 186,550 57,017,708 411,956,831 ddbjcon1.DAD 238,240 97,616,597 1,500,001,746 ddbjcon2.DAD 434,011 172,355,358 1,500,002,756 ddbjcon3.DAD 476,339 173,020,062 1,500,001,413 ddbjcon4.DAD 237,110 97,175,696 1,500,006,334 ddbjcon5.DAD 302,870 115,295,610 1,500,001,981 ddbjcon6.DAD 419,089 167,188,830 1,500,000,150 ddbjcon7.DAD 479,005 183,248,926 1,500,000,252 ddbjcon8.DAD 461,043 123,322,468 1,500,003,665 ddbjcon9.DAD 374,550 65,341,025 1,500,003,960 ddbjcon10.DAD 375,082 64,268,286 1,500,003,228 ddbjcon11.DAD 374,527 65,175,422 1,500,001,938 ddbjcon12.DAD 374,463 65,330,403 1,500,003,890 ddbjcon13.DAD 374,468 65,461,625 1,500,001,179 ddbjcon14.DAD 374,512 65,397,188 1,500,001,113 ddbjcon15.DAD 374,382 65,345,945 1,500,000,595 ddbjcon16.DAD 371,813 72,720,593 1,500,002,804 ddbjcon17.DAD 369,507 78,524,301 1,500,001,383 ddbjcon18.DAD 370,721 73,263,719 1,499,999,946 ddbjcon19.DAD 368,762 78,982,921 1,500,000,895 ddbjcon20.DAD 371,455 73,637,661 1,500,003,263 ddbjcon21.DAD 365,872 86,207,205 1,500,003,026 ddbjcon22.DAD 365,042 88,220,846 1,500,001,244 ddbjcon23.DAD 365,131 86,842,200 1,500,001,916 ddbjcon24.DAD 358,731 90,250,435 1,485,706,847 ddbjenv.DAD 205,235 40,817,895 383,360,932 ddbjest.DAD 1,163 153,762 2,553,096 ddbjgss.DAD 61 12,916 122,434 ddbjhtc.DAD 91,072 29,130,535 379,225,252 ddbjhtg.DAD 40,938 13,845,058 113,153,436 ddbjhum.DAD 356,979 113,944,178 898,313,465 ddbjinv1.DAD 620,865 183,263,230 1,500,003,390 ddbjinv2.DAD 497,317 121,900,884 1,089,031,633 ddbjmam.DAD 134,283 33,614,070 258,745,205 ddbjpat.DAD 385,370 161,102,753 569,783,595 ddbjphg.DAD 73,709 15,395,733 156,636,620 ddbjpln1.DAD 527,035 182,516,323 1,500,002,182 ddbjpln2.DAD 549,275 149,757,525 1,140,717,339 ddbjpri.DAD 51,076 11,215,934 103,573,221 ddbjrod.DAD 166,590 58,354,747 445,148,528 ddbjsts.DAD 9 812 17,852 ddbjsyn.DAD 71,559 28,149,333 189,117,929 ddbjtpa.DAD 44,775 21,359,374 157,085,178 ddbjtsa.DAD 6,174 1,563,022 12,413,047 ddbjuna.DAD 472 106,418 901,649 ddbjvrl1.DAD 742,989 210,754,247 1,500,002,273 ddbjvrl2.DAD 396,823 123,008,888 834,735,786 ddbjvrt.DAD 515,413 133,055,990 1,116,962,046 ========================================================================= total 19,723,681 5,576,482,211 63,749,335,938 =========================================================================