DNA Data Bank of Japan DNA Database Release 65.0, Mar. 2006, including 55,890,995 entries, 60,564,721,635 bases ------------------------------------------------------------------------------- Table of contents ------------------------------------------------------------------------------- 1. Introduction 1.1. Announcement for changes in the present release 1.2. Announcement for the forthcoming changes 2. DDBJ flat file format 2.1. LOCUS line 2.2. DEFINITION line 2.3. ACCESSION line 2.4. VERSION line 2.5. KEYWORDS line 2.6. SOURCE line 2.7. REFERENCE line 2.8. COMMENT line 2.9. FEATURES line 2.10. BASE COUNT line 2.11. ORIGIN line 3. Dataset categories 3.1. Division categories 3.2. TPA separated from primary dataset 3.3. Notice for patented data 4. DDBJ staff 5. Acknowledgment 6. File Contents 6.1. File categories 6.2. File types 7. Sample of the contents in each file 7.1. Part of the contents in the file 'ddbjbct1.seq' 7.2. Part of the contents in the file 'ddbjbct1.acc' 7.3. Part of the contents in the file 'ddbjbct1.aut' 7.4. Part of the contents in the directory file 'ddbjbct1.dir' 7.5. Part of the contents in the file 'ddbjbct1.idx' 7.6. Part of the contents in the file 'ddbjbct1.jou' 7.7. Part of the contents in the file 'ddbjbct1.key' 7.8. Part of the contents in the file 'ddbjbct1.org' 7.9. Part of the contents in the short directory file 'ddbjbct1.sdr' 7.10. Part of the contents in the accession number index file 'ddbjacc1.idx' 7.11. Part of the contents in the keyword phrase index file 'ddbjkey1.idx' 7.12. Part of the contents in the journal citation index file 'ddbjjou1.idx' 7.13. Part of the contents in the gene name index 'ddbjgen.idx' 8. Release history 9. File list ------------------------------------------------------------------------------- 1. Introduction This database contains nucleotide sequence data for any organism, not only those with DNA genomes but also those with RNA genomes. 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. See also '3.3. Notice for patented data' below. The present release contains the newest data prepared by the DNA Data Bank of Japan (DDBJ), GenBank (*), and European Molecular Biology Laboratory/European Bioinformatics Institute (EMBL/EBI) as of February 23, 2006. This unified database was made possible thanks to the international collaboration among the three data banks. All the entries have accordingly been annotated using the feature keys common to them. *'GenBank' is a trademark of NIH, USA, and is operated by National Center for Biotechnology Information (NCBI) at NIH. 1.1. Announcement for changes in the present release Introduction of two types of TPA entries: According to the decision of ICM 2005, TPA data set is now classified into two categories, "TPA:experimental" and "TPA:inferential", to distinguish TPA annotation supported by wet-lab. experimental evidence and that inferred. The retrofit to divide TPA entries into two categories starts from the present release, however, the end point of this retrofit has yet been determined. You can find the description of the two TPA categories at the following URLs; http://www.ddbj.nig.ac.jp/sub/tpa-e.html http://www.insdc.org/TPA.html See also '3.2. TPA separated from primary dataset'. 1.2. Announcement for the forthcoming changes The document, DDBJ/EMBL/GenBank Feature Table: Definition, will be revised in April, 2006. The major point revised is as follows; - Change in Ascidian Mitochondrial Code (transl_table=13) Three alternative initiation codons (ATA, GTG and TTG) are available. See also '2.9. FEATURES line' below. 2. DDBJ flat file format The database is a collection of "entry" which is the unit of the data. The entries submitted to databanks were processed and publicized according to the DDBJ format for distribution (flat file). The flat file includes the sequence and the information of submitters, references, source organisms, and "feature" information, etc. The items of the DDBJ flat file are explained at following; ------------------------------------------------------------------------------- LOCUS AB000000 450 bp mRNA linear HUM 08-JUL-2002 DEFINITION Homo sapiens GAPD mRNA for glyceraldehyde-3-phosphate dehydrogenase, partial cds. ACCESSION AB000000 VERSION AB000000.1 KEYWORDS . SOURCE Homo sapiens ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 450) AUTHORS Mishima,H. and Shizuoka,T. TITLE Direct Submission JOURNAL Submitted (30-NOV-2000) to the DDBJ/EMBL/GenBank databases. Hanako Mishima, National Institute of Genetics, DNA Data Bank of Japan; Yata 1111, Mishima, Shizuoka 411-8540, Japan (E-mail:mishima@supernig.nig.ac.jp, Tel:81-55-981-6853, Fax:81-55-981-6849) REFERENCE 2 (sites) AUTHORS Mishima,H., Shizuoka,T. and Fuji,I. TITLE Glyceraldehyde-3-phosphate dehydrogenase expressed in human liver JOURNAL Unpublished (2002) COMMENT Human cDNA sequencing project. FEATURES Location/Qualifiers source 1..450 /chromosome="12" /clone="GT200015" /clone_lib="lambda gt11 human liver cDNA (GeneTech. No.20)" /map="12p13" /mol_type="mRNA" /organism="Homo sapiens" /tissue_type="liver" CDS 86..>450 /codon_start=1 /gene="GAPD" /product="glyceraldehyde-3-phosphate dehydrogenase" /protein_id="BAA12345.1" /transl_table=1 /translation="MAKIKIGINGFGRIGRLVARVALQSDDVELVAVNDPFITTDYMT YMFKYDTVHGQWKHHEVKVKDSKTLLFGEKEVTVFGCRNPKEIPWGETSAEFVVEYTG VFTDKDKAVAQLKGGAKKV" BASE COUNT 102 a 119 c 131 g 98 t ORIGIN 1 cccacgcgtc cggtcgcatc gcacttgtag ctctcgaccc ccgcatctca tccctcctct 61 cgcttagttc agatcgaaat cgcaaatggc gaagattaag atcgggatca atgggttcgg 121 gaggatcggg aggctcgtgg ccagggtggc cctgcagagc gacgacgtcg agctcgtcgc 181 cgtcaacgac cccttcatca ccaccgacta catgacatac atgttcaagt atgacactgt 241 gcacggccag tggaagcatc atgaggttaa ggtgaaggac tccaagaccc ttctcttcgg 301 tgagaaggag gtcaccgtgt tcggctgcag gaaccctaag gagatcccat ggggtgagac 361 tagcgctgag tttgttgtgg agtacactgg tgttttcact gacaaggaca aggccgttgc 421 tcaacttaag ggtggtgcta agaaggtctg // ------------------------------------------------------------------------------- 2.1. LOCUS line The format of LOCUS line in the flat file is shown below; --------- -------- 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 'bp' 44-47 spaces 48-54 DNA, RNA, mRNA, pre-RNA, rRNA, scRNA, snRNA, snoRNA, tRNA, left justified 55-55 space 56-63 'linear' followed by two spaces, or 'circular' 64-64 space 65-67 The division code (see '3.1. Division categories') 68-68 space 69-79 Date, in the form dd-MMM-yyyy (e.g., 08-JUL-2002) ------------------------------------------------------------------------------ 2.2. DEFINITION line The definition briefly describes the information of gene(s). "DEFINITION" is constructed by each of the three data banks. 2.3. ACCESSION line This line shows accession number of the entry data. A unique accession number is issued to the data submitter by each of the three data banks. The accession number is composed of 1 alphabet character and 5 digits (ex. A12345) or 2 alphabet characters and 6 digits (ex. AB123456). The former style was used in 1980s, but later the latter style was introduced because of data explosion. All the entries designated by the accession numbers with the prefixes given below have been collected and processed by DDBJ, and the rest have been done by GenBank and EMBL/EBI. ------------------------------------------------------------------------------- C, D, E, AB, AG, AK, AP, AT, AU, AV, BA, BB, BD, BJ, BP, BR, BS, BW, BY, CI, CJ, DA, DB, DD, DE ------------------------------------------------------------------------------- You can find the list of the prefixes of the accession numbers at the following URL; http://www.ddbj.nig.ac.jp/sub/prefix.html If multiple entries are united to an entry, or if an entry is extensively modified after the submission, the responsible data banks may assign a new accession number to it. In these cases, the new accession number is called the primary accession number, and the old accession number(s) is/are called the secondary accession number(s). In the flat file, the primary accession number is indicated first, then the secondary accession number(s) follows. You can find the same updated entry with both the primary and the secondary accession numbers. 2.4. VERSION line This line consists of an accession number and a version number, like "AB123456.1", in which the digit(s) after the period is a version number. The data open to public for the first time is version number as "1". The reason for adding VERSION is that since a released sequence sometimes revised by the submitter, the accession number alone cannot specify the sequence in question causing the user a trouble. The number is increased by one every time when a revised sequence is made public. 2.5. KEYWORDS line The data banks describe this line, if necessary. In many cases, the categories of the data (EST, HTG etc.), gene names and product names included in "KEYWORDS". 2.6. SOURCE line This line shows the scientific name on organism from which the sequence is obtained and an organelle type if the sequence is derived from an organelle other than the nucleus. 2.7. REFERENCE line The information on the submitters and references related to the submitted sequence is indicated in REFERENCE line. 2.8. COMMENT line. The information about an entry that can not be described using FEATURES or the other fields. 2.9. FEATURES line Biological features of a submitted sequence data are described with "Feature" key (the biological nature of the annotated feature), "Location" (the region of the sequence which corresponds to Feature), and "Qualifier" (supplementary information about Feature). The "Feature" and "Qualifier" keys used in the present release is defined by DDBJ/EMBL/GenBank Feature Table: Definition (Version 6.4 October, 2005). The document is continuously updated every half year. You can find its newest version on URL; http://www.ddbj.nig.ac.jp/FT/full_index.html 2.10. BASE COUNT line In the BASE COUNT line of the DDBJ flat file, 9 digits are allocated for each number of a (adenine), c (cytosine), g(guanine) and t (thymine). In the case of RNA sequence, uracil is indicated as "t" according to the rule of the international nucleotide database. In accordance with the relaxation of sequence length limitation, GenBank had already dropped the BASE COUNT line from their flat file format from GenBank Release 138 (Oct. 2003). DDBJ has decided to maintain the BASE COUNT line in our flat file format from the view that GC contents are still important information to characterize the sequence. 2.11. ORIGIN line The sequence data starts from the next line of ORIGIN. The sequence is indicated as lower case letters, delimited by space per 10 bases, starts a new line by 60 bases. The numbers described at left side of lines mean the ordinal number of the top base of the line. 3. Dataset categories There have been a number of genome projects going on worldwide. Among them human genome projects have probably been most productive and yielded a large number of ordinary sequences, huge amounts of genome sequences and EST (expressed sequence tags). Thus, we DDBJ have the human (HUM) division solely for human sequences and the primate (PRI) division for non-human primate sequences, while PRI division of GenBank database contains human sequences too. Note that the other divisions such as EST, GSS, and HTC may also contain human sequences. The present release is divided into 21 categories of organisms and others. See also '6.1. File categories' and '9. File list' below. The contents of the 21 categories are shown in the following. 3.1. Division categories The first 20 divisions are given below; HUM; human PRI; primates (other than human) ROD; rodents MAM; mammals (other than primates and rodents) VRT; vertebrates (other than mammals) INV; invertebrates (animals other than vertebrates) PLN; plants, fungi, plastids (eukaryotes other than animals) BCT; bacteria (including both Eubacteria and Archaea) VRL; viruses PHG; bacteriophages ENV; sequences obtained via environmental sampling methods SYN; synthetic constructs EST; expressed sequence tags; short single pass cDNA sequences GSS; genome survey sequences; short single pass genomic sequences HTC; high throughput cDNA sequences; The sequence submitted from full length cDNA sequencing projects. This division is to include unfinished high throughput cDNA sequences, each of which has 5'UTR and 3'UTR at both ends and part of a coding region. The sequence may also include introns. When the sequence becomes finished later, it moves to the corresponding taxonomic division. HTG; high throughput genomic sequences The sequence submitted mainly from genome sequencing projects which regarded a clone as a sequencing unit. STS; sequence tagged sites The tag site for genome sequencing. The information of chromosome, map, PCR_condition is mandatory for this division. PAT; patented data The data submitted to JPO (Japan Patent Office), EPO (European Patent Office), or USPTO (United States Patent and Trademark Office). See also '3.3. Notice for patented data' in below. UNA; the data not annotated The UNA division is not used for recently submitted sequences. CON; Contig / Constructed To conjugate a series of entries, such as those submitted from a genome project, each of data banks constructs an entry and assign an accession number to a large scale sequence dataset. Such entries are classified into the CON division. The entry in the CON division has the information of joined accession numbers instead of the sequence data. The corresponding entries of the CON entry have been submitted to other divisions. The entries and bases in the CON division are not counted in the released numbers given on the top of the release note. 3.2. TPA separated from primary dataset TPA (Third Party Annotation) data are also available. The TPA data are a complement to the existing DDBJ/EMBL/GenBank comprehensive database of primary nucleotide sequences, which typically result from direct sequencing of cDNAs, ESTs, genomic DNAs etc. Primary entries are defined to be data for which the submitting group has done the sequencing and annotation, and as 'owner' of these data has privileges to submit updates/corrections etc. Primary entries used to build a TPA sequence are those that have been experimentally determined and are publicly available in the DDBJ/EMBL/GenBank databases. They may not be from a proprietary database. The entries and bases in TPA are not counted in the released numbers given on the top of the release note. See also the following URLs; http://www.ddbj.nig.ac.jp/sub/tpa-e.html http://www.insdc.org/TPA.html 3.3. Notice for patented data This release includes PAT division for patented data as described above. The patented data are those which the Japanese Patent Office (JPO), United States Patent and Trademark Office (USPTO), and the European Patent Office (EPO) collected, processed and released. The prefixes of accession numbers for the patented data are shown below; ----------------------- JPO : E, BD, DD USPTO: I, AR EPO : A, AX, CQ, CS ----------------------- Note also that unauthorized use of the patented data may cause legal issues for which DDBJ takes no responsibility. 4. DDBJ staff This release is published by the following DDBJ staff. Gojobori T, Tateno Y, Nishikawa K, Sugawara H, Saitou N, Okubo K, Ikeo K, Suzuki Y, Fukuchi S, Kinjo A, Barrero R, Abe T, Sumiyama K, Ogasawara O, Aono H, Atsumi T, Ejima M, Fukuda D, Gojobori M, Hikino Y, Hirai T, Honda K, Hoshi N, Ichikawa K, Ishida K, Kato T, Kawamoto T, Kohira J, Koike T, Kosuge T, Kusakabe A, Kuwana Y, Li C, Lin Y, Maesako H, Mamiya K, Maruyama N, Mashima J, Miyazawa S, Mizunuma T, Murakata N, Nagira S, Nagura M, Nishida S, Nishinomiya N, Nozaki A, Okido T, Sakai K, Shigemoto Y, Shiozawa H, Sugiyama F, Suzuki S, Tsuboi M, Tsutsui H, Yamada H, Yamamoto M, and Yokoyama E 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) ddbjsub@ddbj.nig.ac.jp (for data submission) ddbjupdt@ddbj.nig.ac.jp (for updates and notification of publication) WWW: http://www.ddbj.nig.ac.jp/ (for DDBJ WWW server) http://sakura.ddbj.nig.ac.jp/ (for DDBJ sequence data submission system) 5. Acknowledgment We are grateful to NCBI and EMBL/EBI for a firm friendship and an excellent collaboration with us. We also thank the Japanese Patent Office for a steady cooperation with us. The operation of DDBJ is supported by the Ministry of Education, Culture, Sports, Science and Technology, and we would gratefully note this here. DDBJ uses the Super-SINET computer network for data collection, data exchange and various services. 6. File Contents 6.1. File categories This release covers 21 categories (see also '3. Dataset categories'.) of organisms and others as follows: ------------------------------------------------------------------------------ ddbjbct*** Category for bacteria ddbjcon*** Category for CON (contig sequences) 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 Annotation) 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***.seq files, each of which at most has 300 MB storage capacity as follows, respectively. --------------------- ddbjbct : 11 files ddbjenv : 2 files ddbjest : 394 files ddbjgss : 137 files ddbjhtc : 8 files ddbjhtg : 66 files ddbjhum : 23 files ddbjinv : 7 files ddbjmam : 2 files ddbjpat : 20 files ddbjpln : 14 files ddbjpri : 2 files ddbjrod : 20 files ddbjsts : 12 files ddbjvrl : 5 files ddbjvrt : 9 files --------------------- 6.2. File types The index files included in this release are ddbjacc#.idx, ddbjgen.idx, ddbjjou#.idx, and ddbjkey#.idx. All of them except ddbjgen.idx are recorded in multiple ddbj****.idx files, each of which at most has 1.5 GB storage capacity. We have also included a program by which to make the index files not presented in this release. For the use of the program, see the files, seq2indexes.doc, seq2indexes.c, and seq2indexes.h in this release. Each category then has the following nine types of files. Note that all the files except for ddbj***.seq are created by the user by use of seq2indexes as mentioned above. ------------------------------------------------------------------------------ ddbj***.seq List of an entry in DDBJ format, see 7.1. ddbj***.acc List of the accession numbers, see 7.2. ddbj***.aut List of the authors, see 7.3. ddbj***.dir List of the short directory in DDBJ style, see 7.4. ddbj***.idx List of indices, see 7.5. ddbj***.jou List of the journals, see 7.6. ddbj***.key List of the key words, see 7.7. ddbj***.org List of the species names, see 7.8. ddbj***.sdr List of the short directory in DDBJ style, see 7.9. ------------------------------------------------------------------------------ 7. Sample of the contents in each file 7.1. Part of the contents in the file 'ddbjbct1.seq' This shows all pieces of information on one entry in DDBJ format. ------------------------------------------------------------------------------ LOCUS D87069 993 bp mRNA linear BCT 14-APR-2000 DEFINITION Escherichia coli mRNA for RNA polymerase sigma subunit, truncated form of sigma-38, complete cds. ACCESSION D87069 VERSION D87069.1 KEYWORDS RNA polymerase sigma subunit, truncated form of sigma-38. SOURCE Escherichia coli ORGANISM Escherichia coli Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae; Escherichia. REFERENCE 1 (bases 1 to 993) AUTHORS Jishage,M. TITLE Direct Submission JOURNAL Submitted (14-AUG-1996) to the DDBJ/EMBL/GenBank databases. Miki Jishage, National Institute of Genetics, Molecular Genetics; Yata 1111, Mishima, Shizuoka 411, Japan (E-mail:mjishage@lab.nig.ac.jp, Tel:0559-81-6742, Fax:0559-81-6746) REFERENCE 2 (bases 1 to 993) AUTHORS Jishage,M. and Ishihama,A. TITLE Variation in RNA polymerase sigma subunit composition within different stocks of Escherichia coli starin W3110 JOURNAL Unpublished (1996) REFERENCE 3 AUTHORS Ivanova,A., Renshaw,M., Guntaka,R. and Eisenstark,A. TITLE DNA base sequence variability in katF (putative sigma factor) gene Escherichia coli JOURNAL Nucleic Acids Res. 20, 5479-5480 (1992) REFERENCE 4 AUTHORS Takayanagi,Y., Tanaka,K. and Takahashi,H. TITLE Structure of the 5' upstream region and the regulation of the rpoS gene of Escherichia coli JOURNAL Mol. Gen. Genet. 243, 525-531 (1994) COMMENT FEATURES Location/Qualifiers source 1..993 /mol_type="mRNA" /organism="Escherichia coli" /strain="W3110" CDS 1..810 /note="the gene has four single base changes, resulting in two amino acid substitutions and an amber mutation" /product="RNA polymerase sigma subunit, truncated form of sigma-38" /protein_id="BAA13238.1" /transl_table=11 /translation="MSQNTLKVHDLNEDAEFDENGVEVFDEKALVEYEPSDNDLAEEE LLSQGATQRVLDATQLYLGEIGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLV VKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMN QTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER ITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK" variation 75 /citation=[3] /replace="t" variation 97 /citation=[3] /replace="t" variation 99 /citation=[3] /replace="t" variation 808 /citation=[3] /replace="t" BASE COUNT 254 a 223 c 291 g 225 t ORIGIN 1 atgagtcaga atacgctgaa agttcatgat ttaaatgaag atgcggaatt tgatgagaac 61 ggagttgagg tttttgacga aaaggcctta gtagaatatg aacccagtga taacgatttg 121 gccgaagagg aactgttatc gcagggagcc acacagcgtg tgttggacgc gactcagctt 181 taccttggtg agattggtta ttcaccactg ttaacggccg aagaagaagt ttattttgcg 241 cgtcgcgcac tgcgtggaga tgtcgcctct cgccgccgga tgatcgagag taacttgcgt 301 ctggtggtaa aaattgcccg ccgttatggc aatcgtggtc tggcgttgct ggaccttatc 361 gaagagggca acctggggct gatccgcgcg gtagagaagt ttgacccgga acgtggtttc 421 cgcttctcaa catacgcaac ctggtggatt cgccagacga ttgaacgggc gattatgaac 481 caaacccgta ctattcgttt gccgattcac atcgtaaagg agctgaacgt ttacctgcga 541 accgcacgtg agttgtccca taagctggac catgaaccaa gtgcggaaga gatcgcagag 601 caactggata agccagttga tgacgtcagc cgtatgcttc gtcttaacga gcgcattacc 661 tcggtagaca ccccgctggg tggtgattcc gaaaaagcgt tgctggacat cctggccgat 721 gaaaaagaga acggtccgga agataccacg caagatgacg atatgaagca gagcatcgtc 781 aaatggctgt tcgagctgaa cgccaaatag cgtgaagtgc tggcacgtcg attcggtttg 841 ctggggtacg aagcggcaac actggaagat gtaggtcgtg aaattggcct cacccgtgaa 901 cgtgttcgcc agattcaggt tgaaggcctg cgccgtttgc gcgaaatcct gcaaacgcag 961 gggctgaata tcgaagcgct gttccgcgag taa // ------------------------------------------------------------------------------ 7.2. Part of the contents in the file 'ddbjbct1.acc' The first column refers to the secondary accession number, second column to the locus name, and third to the primary accession number. The primary number may be the same as the secondary number. They are arranged in the ascending order of the secondary accession numbers. ------------------------------------------------------------------------------ D00681 -> AB028210 AB028210 D10012 -> AB010832 AB010832 D10013 -> AB010832 AB010832 D10048 -> AB008452 AB008452 D13563 -> AB018435 AB018435 D13614 -> AB006206 AB006206 D13762 -> AB063629 AB063629 D14537 -> AB040412 AB040412 D14604 -> AB001637 AB001637 D14607 -> AB027308 AB027308 ------------------------------------------------------------------------------ 7.3. Part of the contents in the file 'ddbjbct1.aut' For each author name given on the left to the arrow, the corresponding locus name and primary accession number are respectively listed on the right. They are arranged in the alphabetical order of the author names. ------------------------------------------------------------------------------ Aarestrup,F.M.Threlfall,E.J. -> AF393510 AF393510 Aarnikunnas,J. -> AY090766 AY090766 Aarnio,T. -> AY792975 AY792975 Aarnio,T. -> AY792976 AY792976 Aarnio,T. -> AY792977 AY792977 Aarnio,T. -> AY792978 AY792978 Aarnio,T. -> AY792979 AY792979 Aarnio,T. -> AY792980 AY792980 Aarnio,T. -> AY792981 AY792981 Aarnio,T. -> AY792982 AY792982 ------------------------------------------------------------------------------ 7.4. Part of the contents in the directory file 'ddbjbct1.dir' For each locus name given in the first column, the corresponding primary accession number, molecular type, number of nucleotide pairs, and description for the locus are respectively listed. They are arranged in the alphabetical order of the locus names. ------------------------------------------------------------------------------ AAC133631 AJ133631 DNA 1482 Alicyclobacillus acidoterrestris 16S rRNA gene, strain DSM 3922T. AAC133789 AJ133789 DNA 3097 Alicyclobacillus acidocaldarius cyclomaltodex trinase gene region. AAC243194 AJ243194 DNA 1720 Alicyclobacillus acidocaldarius kdpA gene. AAC252160 AJ252160 DNA 1638 Alicyclobacillus acidocaldarius cysA gene for putative ABC-transporter ATP-binding protein. AAC252161 AJ252161 DNA 8690 Alicyclobacillus acidocaldarius maltose/maltodextrine transport gene region (malEFGR genes, cdaA gene and glcA gene). AAC289685 AJ289685 DNA 453 Actinobacillus actinomycetemcomitans partial infB gene for translation initiation factor IF2, strain CCUG13227 T (ATCC33384, NCTC9710). AAC289686 AJ289686 DNA 453 Actinobacillus actinomycetemcomitans partial infB gene for translation initiation factor IF2, strain HK666. AAC289687 AJ289687 DNA 453 Actinobacillus actinomycetemcomitans partial infB gene for translation initiation factor IF2, strain HK1662. AAC289694 AJ289694 DNA 453 Actinobacillus actinomycetemcomitans partial infB gene for translation initiation factor IF2, strain HK1651. ------------------------------------------------------------------------------ 7.5. Part of the contents in the file 'ddbjbct1.idx' The first column refers to the locus name, second column to the starting site of the locus in byte, and third to its ending site in byte. They are arranged in the alphabetical order of the locus names. ------------------------------------------------------------------------------ %***************************** #AAC133631 1125664347 1125667802 #AAC133789 1125786300 1125794416 #AAC243194 1136871421 1136876093 #AAC252160 1146107711 1146112332 #AAC252161 1146112333 1146131350 #AAC289685 1155353186 1155356047 #AAC289686 1155356048 1155358781 #AAC289687 1155358782 1155361517 #AAC289694 1155377972 1155380768 #AAC308623 1167555889 1167560983 ------------------------------------------------------------------------------ 7.6. Part of the contents in the file 'ddbjbct1.jou' This gives information on the journal in which sequence data were published. ------------------------------------------------------------------------------ Yi Chuan Xue Bao 29 (12), 1111-1117 (2002) -> AY601668 AY601668 Yi Chuan Xue Bao 29 (12), 1111-1117 (2002) -> AY603420 AY603420 Yi Chuan Xue Bao 30 (4), 364-369 (2003) -> AF526379 AF526379 Yonsei Med. J. 39 (6), 520-525 (1998) -> AF373217 AF373217 Yonsei Med. J. 39 (6), 520-525 (1998) -> AF373218 AF373218 Z. Lebensm.-Unters. -Forsch., A Eur. Food Res. Technol. 209, 83-87(1999). -> ABA7623 AJ007623 Z. Lebensm.-Unters. -Forsch., A Eur. Food Res. Technol. 209, 83-87(1999). -> ABA7624 AJ007624 Zb. Bioteh. Fak. Univ. Ljubl. Kmet. Supl. 79(1), 107-113(2002). -> ASP012466 AJ012466 Zb. Bioteh. Fak. Univ. Ljubl. Kmet. Supl. 79(1), 19-26(2002). -> ASP012466 AJ012466 Zentralbl. Bakteriol. 286 (1), 1-8 (1997) -> AF192489 AF192489 Zentralbl. Bakteriol. 290, 37-49(2000). -> LPN7311 AJ007311 Zentralbl. Bakteriol. 291, 345-352(2001). -> LPN300467 AJ300467 Zentralbl. Bakteriol. 292, 207-214(2002). -> ECO459584 AJ459584 Zhi Wu Bao Hu Xue Hui Hui Kan 44, 233-244 (2002) -> AF540014 AF540014 Zhi Wu Bing Li Xue Bao 34 (1), 80-85 (2004) -> AY447045 AY447045 Zhi Wu Bing Li Xue Hui Kan 12, 57-64 (2003) -> AF450275 AF450275 Zhiwu Baohuxue Hui Huikan 44, 185-208 (2002) -> AY122057 AY122057 Zhiwu Binglixue Huikan 6, 207-208 (1997) -> AF149819 AF149819 Zhongguo Jiaqin 25 (Supplement 1), 60-71 (2003) -> AY615358 AY615358 Zhongguo Kang Sheng Su Za Zhi 21, 94-97 (2003) -> AY293073 AY293073 Zhongguo Kang Sheng Su Za Zhi 28, 96-100 (2003) -> AY293071 AY293071 Zhongguo Kang Sheng Su Za Zhi 28, 96-100 (2003) -> AY293072 AY293072 Zhongguo Lin Chuang Yao Li Xue Za Zhi 19, 190-195 (2003) -> AY536040 AY536040 Zhongguo Nong Ye Ke Xue 36(1), 17-25 (2003) -> AY555768 AY555768 Zhonghua Liu Xing Bing Xue Za Zhi 24, 291-295 (2003) -> AY279003 AY279003 Zhonghua Min Guo Wei Sheng Wu Ji Mian Yi Xue Za Zhi (2003) In press -> AY299484 AY299484 Zhonghua Min Guo Wei Sheng Wu Ji Mian Yi Xue Za Zhi 22 (5), 489-492 (2002) -> AY382160 AY382160 Zool. Sci. 14, 701-706 (1997) -> AB002286 AB002286 Zool. Sci. 14, 701-706 (1997) -> AB002287 AB002287 Zool. Sci. 14, 701-706 (1997) -> AB002288 AB002288 Zool. Sci. 14, 701-706 (1997) -> AB002289 AB002289 Zool. Sci. 14, 701-706 (1997) -> AB002290 AB002290 Zool. Sci. 14, 701-706 (1997) -> AB002291 AB002291 Zoolog. Sci. 17, 983-989 (2000) -> AB038366 AB038366 Zoolog. Sci. 17, 983-989 (2000) -> AB038367 AB038367 Zoolog. Sci. 17, 983-989 (2000) -> AB038368 AB038368 Zoolog. Sci. 17, 983-989 (2000) -> AB038369 AB038369 Zoolog. Sci. 17, 983-989 (2000) -> AB038370 AB038370 ------------------------------------------------------------------------------ 7.7. Part of the contents in the file 'ddbjbct1.key' For the locus and accession number respectively given on the right to the arrow, the corresponding keywords are listed on the left. ------------------------------------------------------------------------------ Synechococcus sp. DNA for intrinsic membrane protein, malK-like protein, cyanase, complete cds. -> AB000100 AB000100 cynS; cyanase; cynD; malK-like protein; cynB; intrinsic membrane protein. -> AB000100 AB000100 Direct Submission -> AB000100 AB000100 Identification and nitrogen regulation of the cyanase gene from the cyanobacteri a Synechocystis sp. strain PPC 6803 and Synechococcus sp. strain PPC 7942 -> AB000100 AB000100 Sequence updated (31-Mar-1997) by: Tatsuo Omata Sequence updated (14-Aug-1997) -> AB000100 AB000100 Sphingomonas sp. 16S ribosomal RNA. -> AB000106 AB000106 16S rRNA. -> AB000106 AB000106 Direct Submission -> AB000106 AB000106 Sphingomonas sp. VT1 16s rRNA -> AB000106 AB000106 Synechococcus sp. gene for ribosomal proteins, complete cds. -> AB000111 AB000111 tRNA pseudouridine synthase I; 50S ribosomal protein L17; DNA-dircted RNA polymerase alpha chain; 30S Ribosomal Protein S11; 30S ribosomal protein S13; 50S ribosomal protein L36; adenylate kinase; preprotein translocase SecY subunit; 50S ribosomal protein L15; 30S ribosomal protein S5; 50S ribosomal protein L18; 50S ribosomal protein L6; 30S ribosomal protein S8; 50S ribosomal protein L5; 50S ribosomal protein L24; 50S ribosomal protein L14; 30S ribosomal protein S17; 50S ribosomal protein L29; 50S ribosomal protein L16; 30S ribosomal protein S3; 50S ribosomal protein L22; 30S ribosomal protein S19; 50S ribosomal protein L2; 50S ribosomal protein L23; 50S ribosomal protein L4; 50S ribosomal protein L3. -> AB000111 AB000111 Direct Submission -> AB000111 AB000111 ------------------------------------------------------------------------------ 7.8. Part of the contents in the file 'ddbjbct1.org' For the locus and accession number respectively given on the right to the arrow, the corresponding taxonomic names are listed on the left. They are arranged in the alphabetical order of the species names. ------------------------------------------------------------------------------ 'Flavobacterium' lutescens 'Flavobacterium' lutescens Bacteria; Proteobacteria; gamma subdivision; Pseudomonadaceae; Pseudomonas. -> AB035478 AB035478 'Flavobacterium' lutescens 'Flavobacterium' lutescens Bacteria; Proteobacteria; gamma subdivision; Pseudomonadaceae; Pseudomonas. -> AB042983 AB042983 'Fragaria multicipita' phytoplasma 'Fragaria multicipita' phytoplasma Bacteria; Firmicutes; Mollicutes; Acholeplasmatales; Acholeplasmataceae; Candidatus Phytoplasma. -> AF036354 AF036354 'Fragaria multicipita' phytoplasma 'Fragaria multicipita' phytoplasma Bacteria; Firmicutes; Mollicutes; Acholeplasmatales; Acholeplasmataceae; Candidatus Phytoplasma. -> AF190224 AF190224 'Fragaria multicipita' phytoplasma 'Fragaria multicipita' phytoplasma Bacteria; Firmicutes; Mollicutes; Acholeplasmatales; Acholeplasmataceae; Candidatus Phytoplasma. -> AF190225 AF190225 'Helichrysum bracteatum' phytoplasma 'Helichrysum bracteatum' phytoplasma Bacteria; Firmicutes; Mollicutes; Acholeplasmatales; Acholeplasmataceae; Candidatus Phytoplasma. -> AF515771 AF515771 'Momordica charantia' phytoplasma 'Momordica charantia' phytoplasma Bacteria; Firmicutes; Mollicutes; Acholeplasmatales; Acholeplasmataceae; Candidatus Phytoplasma. -> PHY431368 AJ431368 'Rehmannia glutinosa var. purpurea' phytoplasma 'Rehmannia glutinosa var. purpurea' phytoplasma Bacteria; Firmicutes; Mollicutes; Acholeplasmatales; Acholeplasmataceae; Candidatus Phytoplasma. -> AF335107 AF335107 'Rhizomonas' sp. 'Rhizomonas' sp. Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingomonas. -> UBA132327 AJ132327 'Vinca minor' phytoplasma 'Vinca minor' phytoplasma Bacteria; Firmicutes; Mollicutes; Acholeplasmatales; Acholeplasmataceae; Candidatus Phytoplasma. -> AY144608 AY144608 ------------------------------------------------------------------------------ 7.9. Part of the contents in the short directory file 'ddbjbct1.sdr' The short directory file contains brief descriptions of all of the sequence entries contained in the DDBJ style. ------------------------------------------------------------------------------ AC133631 Alicyclobacillus acidoterrestris 16S rRNA gene, strain DSM 1482bp AAC133789 Alicyclobacillus acidocaldarius cyclomaltodextrinase gene 3097bp AAC243194 Alicyclobacillus acidocaldarius kdpA gene. 1720bp AAC252160 Alicyclobacillus acidocaldarius cysA gene for putative 1638bp AAC252161 Alicyclobacillus acidocaldarius maltose/maltodextrine 8690bp AAC289685 Actinobacillus actinomycetemcomitans partial infB gene for 453bp AAC289686 Actinobacillus actinomycetemcomitans partial infB gene for 453bp AAC289687 Actinobacillus actinomycetemcomitans partial infB gene for 453bp AAC289694 Actinobacillus actinomycetemcomitans partial infB gene for 453bp AAC308623 Alicyclobacillus acidocaldarius celA gene for cellulase. 1778bp AAC417690 Actinobacillus actinomycetemcomitans mukB gene. 4491bp AAC419840 Acetobacter aceti 16S rRNA gene, strain LMG 1531. 1440bp AAC430786 Actinobacillus actinomycetemcomitans partial fur gene for 1246bp AAC493667 Alicyclobacillus acidocaldarius subsp. rittmannii 16S rRNA 1472bp AAC496806 Alicyclobacillus acidocaldarius 16S rRNA gene, strain DSM 1507bp ------------------------------------------------------------------------------ In addition to the tables for the four following index files are included in this release. These files were prepared for BCT, ENV, EST, GSS, HTC, HTG, HUM, INV, MAM, PAT, PHG, PLN, PRI, ROD, STS, SYN, UNA, VRL, and VRT divisions. Accession number index file Keyword phrase index file Journal citation index file Gene name index file A brief description is given for each file in the above section, '3. Dataset categories'. 7.10. Part of the contents in the accession number index file 'ddbjacc1.idx' The following excerpt from the accession number index file illustrates the format of the index. ------------------------------------------------------------------------------ D00001 ECPBPA BCT X04516 D00002 ECPYRC BCT X04469 D00003 HUMP450M HUM D00003 D00004 FLBFLBL40 VRL D00004 D00005 IBAMEM682 VRL D00005 D00006 BACPNS1981 BCT D00006 D00007 CHKCALGRP VRT D00007 D00008 ECPNTAB BCT X04195 D00009 DROPER1 INV D00009 ------------------------------------------------------------------------------ 7.11. Part of the contents in the keyword phrase index file 'ddbjkey1.idx' Keyword phrases consist of names for gene products and other characteristics of sequence entries. ------------------------------------------------------------------------------ "COAT PROTEIN SMO511347 VRL AJ511347 'TNPA GENE UBA564903 BCT AJ564903 'ZINC-FINGER' MOTIF PRNS53 VRL X60546 (+) MATING TYPE SURFACE PROTEIN ABGPSSP PLN M94861 (1,3 TABETGLUB PLN Z22874 (1,3)-BETA-D-GLUCAN BINDING PROTEIN AJ606470 INV AJ606470 (1,3)BETA-GLUCAN SYNTHASE NCU09275 PLN U09275 (1,4)-BETA-D-ARABINOXYLAN ARABINOFURANOHYDROLASE ANAXHA PLN Z78011 ANTUAXHA PLN Z78010 (1,6)-BETA-GLUCAN BIOSYNTHESIS YSAKRE1A PLN M81588 (1-3)-BETA-GLUCANASE NTSP41AGN PLN X81560 PA13BGPT PLN X57794 (1-3,1-4)-BETA-D-GLUCANASE HVBDG PLN X52572 (1-4)-BETA-MANNAN ENDOHYDROLASE CAR278996 PLN AJ278996 CAR293305 PLN AJ293305 (2',5'-OLIGOISOADENYLATE SYNTHETASE-DEPENDENT) AL138776 HUM AL138776 (2'-5') OLIGO(A) SYNTHASE E16 SSO4G06 EST F14610 (2'-5')OLIGOADENYLATE SYNTHETASE HSA225089 HUM AJ225089 HUMSYN25A HUM D00068 SSA225090 MAM AJ225090 (6')-IB' AMINOGLYCOSIDE ACETYLTRANSFERASE AXY278514 BCT AJ278514 PAE291609 BCT AJ291609 (8,11)-LINOLEOYL DESATURASE COF245938 PLN AJ245938 ------------------------------------------------------------------------------ 7.12. Part of the contents in the journal citation index file 'ddbjjou1.idx' The journal citation index file lists all of the citations that appear in the references. ------------------------------------------------------------------------------ (ER) AAPS PHARMSCI. 4 (3), DOI 10.1208/PS040315 (2002) AY170916 ROD AY170916 (ER) AM. J. HUM. GENET. 76 (1) (2004) IN PRESS AY753209S1 HUM AY753209 AY753209S2 HUM AY753210 (ER) ARCH. VIROL. (2004) IN PRESS AF531505 VRL AF531505 AY518899 VRL AY518899 AY518900 VRL AY518900 AY518901 VRL AY518901 AY518902 VRL AY518902 AY518903 VRL AY518903 AY518904 VRL AY518904 AY518905 VRL AY518905 AY518906 VRL AY518906 AY518907 VRL AY518907 AY518908 VRL AY518908 AY518909 VRL AY518909 AY518910 VRL AY518910 AY518911 VRL AY518911 AY518912 VRL AY518912 AY518913 VRL AY518913 AY518914 VRL AY518914 AY518915 VRL AY518915 AY518916 VRL AY518916 AY518917 VRL AY518917 AY518918 VRL AY518918 AY518919 VRL AY518919 AY518920 VRL AY518920 AY518921 VRL AY518921 AY518922 VRL AY518922 AY518923 VRL AY518923 AY518924 VRL AY518924 AY518925 VRL AY518925 AY518926 VRL AY518926 AY518927 VRL AY518927 AY518928 VRL AY518928 AY518929 VRL AY518929 AY518930 VRL AY518930 AY518931 VRL AY518931 AY518932 VRL AY518932 AY521234 VRL AY521234 AY521235 VRL AY521235 AY521236 VRL AY521236 AY521237 VRL AY521237 AY521238 VRL AY521238 (ER) ARTERIOSCLER. THROMB. VASC. BIOL. (2004) IN PRESS AY563557 HUM AY563557 (ER) BIOCHEM. BIOPHYS. RES. COMMUN. 325 (1), 203-214 (2004) AY563137 HUM AY563137 (ER) BIOCHEM. J./10.1042/BJ20030293 HSA496460 HUM AJ496460 ------------------------------------------------------------------------------ 7.13. Part of the contents in the gene name index file 'ddbjgen.idx' This file lists all the gene names that appear in the feature table. ------------------------------------------------------------------------------ 'ARR BX927156 BCT BX927156 'BGLG BX927156 BCT BX927156 'BGLS BX927148 BCT BX927148 'BGLY' BX927156 BCT BX927156 'BRNQ AF305888 BCT AF305888 'COMK AL591983 BCT AL591983 AL596172 BCT AL596172 'CRCB BX927155 BCT BX927155 'CRTI BX927155 BCT BX927155 'DPPE LDDIPEP BCT Z34898 'FIC BX936398 BCT BX936398 ------------------------------------------------------------------------------ 8. Release history Release Date Entries Bases Comments 65 03/06 55,890,995 60,564,721,635 64 12/05 52,272,669 56,098,558,378 Some index files split 63 09/05 47,741,593 52,246,110,341 62 06/05 45,249,444 49,158,155,283 ENV started Version for release note started 61 03/05 43,118,204 47,099,081,750 Changed style of release note 60 12/04 40,583,945 44,416,752,273 /db_xref="H-inv:**" started 59 09/04 37,926,117 42,245,956,937 58 06/04 34,917,581 39,812,635,108 57 03/04 32,693,678 38,008,449,840 56 12/03 30,405,173 36,079,046,032 55 09/03 27,753,140 34,280,225,489 54 06/03 25,149,821 32,162,041,177 53 02/03 23,250,813 29,711,299,332 52 12/02 20,354,812 26,931,456,316 51 09/02 18,401,358 22,782,404,136 TPA started 50 06/02 17,260,693 20,158,357,982 49 04/02 16,503,157 18,579,627,226 48 01/02 15,016,100 16,197,713,855 47 10/01 13,266,610 14,145,671,645 46 07/01 12,313,759 13,037,646,166 45 04/01 11,434,113 12,207,092,905 HTC division started 44 01/01 10,165,597 11,136,298,841 43 10/00 8,666,551 10,034,532,698 42 07/00 7,554,995 8,880,721,093 41 04/00 5,962,608 6,409,581,885 CON division started 40 01/00 5,388,125 4,762,696,173 RNA division terminated 39 10/99 4,810,773 3,728,000,562 NID and PID discarded 38 07/99 4,294,369 3,098,519,597 37 03/99 3,311,627 2,375,261,951 VERSION, /protein_id started 36 01/99 3,073,166 2,190,425,560 35 10/98 2,759,261 1,957,341,169 34 07/98 2,412,785 1,708,580,623 33 04/98 2,174,769 1,479,303,279 32 01/98 1,956,669 1,300,950,613 31 10/97 1,731,532 1,139,869,464 Adoption of the unified taxonomy database 30 07/97 1,534,115 992,788,339 NID and PID terminated 29 04/97 1,270,194 841,415,232 28 01/97 1,154,120 756,785,219 HTG division started ORG division terminated 27 10/96 936,697 608,103,057 GSS division started 26 07/96 835,552 551,932,448 25 04/96 744,490 499,300,364 /translation started 24 01/96 637,508 431,771,652 23 10/95 569,757 390,694,350 22 07/95 437,588 322,982,425 HUM division started 21 04/95 274,596 250,875,023 20 01/95 239,689 231,299,557 19 10/94 204,332 205,274,131 18 07/94 185,230 192,473,021 17 04/94 169,957 179,942,209 16 01/94 154,626 165,017,628 15 10/93 131,649 147,224,690 14 07/93 120,350 138,686,333 13 04/93 112,067 129,784,445 12 01/93 97,683 120,815,244 EST division started 11 07/92 65,693 84,839,075 10 01/92 59,317 77,805,556 GenBank/EMBL inclusion started 9 07/91 1,130 2,002,124 8 01/91 879 1,573,442 7 07/90 681 1,154,211 6 01/90 496 841,236 5 07/89 395 679,378 4 01/89 302 535,985 3 07/88 230 345,850 2 01/88 142 199,392 1 07/87 66 108,970 Started with DDBJ only ------------------ Since release 64 ------------------ Split of index files: In the present release, some of index files (ddbjacc.idx, ddbjjou.idx, and ddbjkey.idx) have been greater than 2 GB in the file size. So, these have been recorded in multiple ddbj****.idx files, each of which at most has 1.5 GB storage capacity as follows, respectively. See also 6.2., 7.10., 7.11., 7.12. and 9. ------------------ Since release 62 ------------------ Release version number is introduced: DDBJ has started to include the item, 'version', for its release note, which indicates a version for its periodical release. It is expressed like '62.0', in which the digit(s) after the period is a version number. The reason for adding the version number is that a released data is sometimes revised due to urgent and necessary corrections. The number is increased by one every time when a revised periodical release is made public until the next release. 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 (See also '3.1. Division categories'). 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. Strand information is removed: The strand information of LOCUS line in the flat file has been removed as shown below. See also '2.1. LOCUS line'. ---------------------------------------------------------------------------- Old (-rel. 61): 44-44 space 45-47 spaces, ss- (single-stranded), ds- (double-stranded), or ms- (mixed-stranded) New (rel. 62-): 44-47 spaces ---------------------------------------------------------------------------- ------------------ Since release 61 ------------------ The style of release note (this file) has been changed. Some entries have the sequential format for the secondary accession numbers in the ACCESSION line, in order to make the expression of secondary accession numbers in the past short. For example; ------------------------------------------------------------------------------ Before; ACCESSION AB000802 D85885 D85886 D85887 After; ACCESSION AB000802 D85885-D85887 ------------------------------------------------------------------------------ See also '2.3. ACCESSION line'. ------------------ Since release 60 ------------------ The cross-reference to the H-invitational has been included. ------------------ Since release 56 ------------------ The three data banks have agreed that the maximum length limitation (350 kb) of a submitted sequence be relaxed. The BASE COUNT line of the DDBJ flat file format has been changed, corresponding to the relaxation of the maximum sequence length restriction in the entry that had been practiced at DDBJ/EMBL/GenBank International Nucleotide Sequence Databases. In the BASE COUNT line of the DDBJ flat file, 6 digits had been allocated for each number of a, c, g, t and other bases in the sequence. Hereafter, in the new flat file format, 9 digits are allocated for each number of a, c, g and t, while the numbers of other bases are removed. In accordance with the relaxation of sequence length limitation, GenBank had already dropped the BASE COUNT line from their flat file format from GenBank Release 138 (Oct. 2003). We DDBJ have decided to maintain the BASE COUNT line in our flat file format from the view that GC contents are still important information to characterize the sequence. The changes in the BASE COUNT line are shown below. ---------------------------------------------------------------------------- Old (-rel. 55): 1 6 11 16 21 26 31 36 41 46 51 56 61 66 71 |----|----|----|----|----|----|----|----|----|----|----|----|----|----| BASE COUNT 123456 a 123456 c 123456 g 123456 t 123456 others New (rel. 56-): 1 6 11 16 21 26 31 36 41 46 51 56 61 66 71 |----|----|----|----|----|----|----|----|----|----|----|----|----|----| BASE COUNT 123456789 a 123456789 c 123456789 g 123456789 t ---------------------------------------------------------------------------- The SOURCE in the flat file is revisited and revised if necessary in accordance with the unified taxonomy database common to the three data banks. ------------------ Since release 54 ------------------ '/sequenced_mol' qualifier has been changed to '/mol_type' qualifier. We accordingly completed retrofitting the pertinent entries. This change was made on the agreement at the INSD collaborative meeting in 2002. ------------------ Since release 51 ------------------ The TPA (Third Party Annotation) dataset has been available. The dataset is a complement to the existing DDBJ/EMBL/GenBank database of the primary nucleotide sequences which were obtained from direct sequencing of cDNAs, ESTs, genomic DNAs etc. The format of LOCUS line in the flat file has been changed as shown below to adjust to the GenBank format. ------------------------------------------------------------------------------ Old (-rel. 50): LOCUS AB000001 660 bp DNA PLN 01-FEB-2001 New (rel. 51-): LOCUS AB000001 660 bp DNA linear PLN 01-FEB-2001 ------------------------------------------------------------------------------ ------------------ Since release 45 ------------------ The HTC (High Throughput cDNA) division has been included. This is to include unfinished high throughput cDNA sequences, each of which has 5'UTR and 3'UTR at both ends and part of a coding region. The sequence may also include introns. When the sequence becomes finished later, it moves to the corresponding taxonomic division. The sequence is accompanied with a keyword, HTC (High Throughput cDNA), which is dropped when the sequence is finished and moved to a taxonomic division. ------------------ Since release 41 ------------------ The CON division has been included. This division is to show the order of related sequences in a genome, and expressed by join and the accession numbers of the sequences. The contents of the CON division are compiled by the three data banks not by the data submitter. ------------------ Since release 40 ------------------ The RNA division was terminated. The RNA data have been redistributed according to the category of the organism. Therefore, you will find a human RNA sequence, for example, in the HUM division. ------------------ Since release 37 ------------------ The three data banks include the item VERSION in the flat file, which indicates a version of a submitted nucleotide sequence. It is expressed like AB123456.1, in which the digit(s) after the period is a version number. The reason for adding VERSION is that since a released sequence sometimes revised by the submitter, the accession number alone cannot specify the sequence in question causing the user a trouble. The number is increased by one every time when a revised sequence is made public. Accordingly, the translated protein sequence will be accompanied with a /protein_id which is expressed as BAA12345.1, in which the digit(s) after the period is again a version number. The number is increased by one when the corresponding nucleotide sequence is revised and the protein sequence is changed as a result, and when the revised protein sequence is made public. ------------------ Since release 31 ------------------ We have started adopting the unified taxonomy database to unify the biological source of the sequence. The database is made up with scientific names, ID of unidentified organisms, and synthetic constructs etc. ------------------ Since release 30 ------------------ NID and PID were terminated. This change was made on the agreement at the INSD collaborative meeting in 1999. ------------------ Since release 28 ------------------ The HTG (High Throughput Genomic sequence) has been included. This division was created to cope with genome project teams which deal with a clone as a sequencing unit. We terminated the ORG (Organelle) division. Thus, if you are interested in human mitochondrial sequences, for example, you are now advised to refer to the HUM division. ------------------ Since release 27 ------------------ The GSS division has been included. GSS stands for Genome Survey Sequence, which is similar to EST, except that GSS is genomic DNA whereas EST is cDNA. ------------------ Since release 25 ------------------ DDBJ release contains amino acid sequences that were translated from the corresponding nucleotide sequences of the database. In the translation we paid much attention to the fact that some species or organella have a codon different from the universal one, and used the proper codon table. ------------------ Since release 22 ------------------ The HUM division has been included. Human genome projects have probably been most productive and yielded a large number of sequences Thus, we have the human (HUM) division solely for human sequences and the primate (PRI) division for non-human primate sequences. ------------------ Since release 12 ------------------ The EST (Expressed Sequence Tag) division has been included. The number of ESTs has been increasing at an enormous rate and is expected to be growing even more rapidly in the future. Thus, we created a division for ESTs ------------------ Since release 10 ------------------ The sequences submitted to GenBank or EMBL have been included in the release. 9. File list The files in this release are arranged in the following order with non-labeled format. ----------------------------------------------------------------------- file name file size ----------------------------------------------------------------------- ddbjrel.txt (DDBJ release note) 108423 ddbjacc1.idx (Accession number index file 1) 1499999962 ddbjacc2.idx (Accession number index file 2) 679517172 ddbjgen.idx (Gene name index file) 83542515 ddbjjou1.idx (Journal citation index file 1) 1432649244 ddbjjou2.idx (Journal citation index file 2) 1059231072 ddbjkey1.idx (Keyword phrase index file 1) 1443779835 ddbjkey2.idx (Keyword phrase index file 2) 727674291 ----------------------------------------------------------------------- file name number of entries number of bases file size ----------------------------------------------------------------------- ddbjbct1.seq 25236 127554497 305595610 ddbjbct2.seq 3767 132430321 302956852 ddbjbct3.seq 5144 130708675 299000465 ddbjbct4.seq 65430 105410558 299018731 ddbjbct5.seq 9803 132597827 305281710 ddbjbct6.seq 67544 109153688 307843017 ddbjbct7.seq 172 134420278 299312772 ddbjbct8.seq 144 132218217 304435823 ddbjbct9.seq 62 133680485 301339916 ddbjbct10.seq 12704 129034106 299000785 ddbjbct11.seq 46667 94057075 251865603 ddbjenv1.seq 112158 83683557 299002709 ddbjenv2.seq 102357 87190785 280409319 ddbjest1.seq 89397 33746774 299000357 ddbjest2.seq 94466 37880239 299002434 ddbjest3.seq 95270 37085652 299003067 ddbjest4.seq 89461 28167866 299000246 ddbjest5.seq 94080 36235692 299002910 ddbjest6.seq 97532 38717660 299002008 ddbjest7.seq 98291 37969476 299001083 ddbjest8.seq 97520 37603757 299001621 ddbjest9.seq 97774 38730361 299002095 ddbjest10.seq 99558 38933438 299001092 ddbjest11.seq 97533 39025831 299000407 ddbjest12.seq 96807 43060369 299000151 ddbjest13.seq 105171 42425486 299003045 ddbjest14.seq 101270 40877874 299002770 ddbjest15.seq 97423 40597820 299000997 ddbjest16.seq 94988 42641211 299001847 ddbjest17.seq 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111503 74454058 299000695 ddbjgss48.seq 113814 62453185 299002288 ddbjgss49.seq 110657 65398843 299002461 ddbjgss50.seq 96016 66798612 299002379 ddbjgss51.seq 92066 60647296 299003131 ddbjgss52.seq 98396 57054978 299002492 ddbjgss53.seq 102102 57618600 299000894 ddbjgss54.seq 109793 77304633 299000027 ddbjgss55.seq 105299 75033612 299000494 ddbjgss56.seq 117228 72972788 299000451 ddbjgss57.seq 104783 66975323 299001779 ddbjgss58.seq 92530 49138539 299002028 ddbjgss59.seq 116636 64456848 299000816 ddbjgss60.seq 110499 57129502 299000354 ddbjgss61.seq 106842 73221101 299001533 ddbjgss62.seq 92111 101052073 299001798 ddbjgss63.seq 109856 88796691 299001253 ddbjgss64.seq 101388 67200752 299000464 ddbjgss65.seq 82363 57625089 299000545 ddbjgss66.seq 109544 81404225 299002247 ddbjgss67.seq 109572 70396705 299000982 ddbjgss68.seq 111657 72426057 299001851 ddbjgss69.seq 116790 75247106 298999996 ddbjgss70.seq 128087 68358249 299000363 ddbjgss71.seq 127706 68859324 299002268 ddbjgss72.seq 129289 66786070 299001802 ddbjgss73.seq 129827 66081901 299001768 ddbjgss74.seq 129485 66527521 299000040 ddbjgss75.seq 128942 67240165 299001710 ddbjgss76.seq 119090 80785887 299000834 ddbjgss77.seq 113899 89670273 299002275 ddbjgss78.seq 111823 88412883 299002439 ddbjgss79.seq 112303 84878138 299000835 ddbjgss80.seq 115960 56912141 299000860 ddbjgss81.seq 118057 35821796 299001131 ddbjgss82.seq 109511 59796744 299002303 ddbjgss83.seq 105007 59875981 299000799 ddbjgss84.seq 113712 81188909 299000921 ddbjgss85.seq 98849 84764931 299003180 ddbjgss86.seq 99862 89445966 299002952 ddbjgss87.seq 114652 63518833 299002389 ddbjgss88.seq 96654 52978350 299001628 ddbjgss89.seq 103662 73629076 298999925 ddbjgss90.seq 102519 70484923 299001820 ddbjgss91.seq 104079 73207072 299001145 ddbjgss92.seq 108671 71671972 299001230 ddbjgss93.seq 110508 67976611 299000639 ddbjgss94.seq 112826 88942436 299001591 ddbjgss95.seq 139613 84733992 299001072 ddbjgss96.seq 134663 87435708 299000912 ddbjgss97.seq 109726 61490626 299000146 ddbjgss98.seq 106705 65467378 299000662 ddbjgss99.seq 118133 84234471 299000802 ddbjgss100.seq 123349 88831057 299002342 ddbjgss101.seq 121409 91189767 299000636 ddbjgss102.seq 119466 91836147 299000625 ddbjgss103.seq 97781 55364426 299001160 ddbjgss104.seq 95125 57482025 299002811 ddbjgss105.seq 94998 57720853 299002353 ddbjgss106.seq 94457 58592973 299001978 ddbjgss107.seq 95043 57374086 299002750 ddbjgss108.seq 104666 69622019 299001667 ddbjgss109.seq 106231 70878877 299002499 ddbjgss110.seq 104577 66251334 299001112 ddbjgss111.seq 107866 66624548 299000021 ddbjgss112.seq 101443 74467902 299001340 ddbjgss113.seq 118963 66492497 299000671 ddbjgss114.seq 100446 63834794 299001553 ddbjgss115.seq 111001 78369713 299001222 ddbjgss116.seq 103455 72961179 299001378 ddbjgss117.seq 96529 58653428 299001027 ddbjgss118.seq 119443 65299207 299001055 ddbjgss119.seq 108829 69940516 299002000 ddbjgss120.seq 109490 71176190 299001751 ddbjgss121.seq 100535 80033207 299000135 ddbjgss122.seq 97153 54249292 299000974 ddbjgss123.seq 116534 57560285 299003222 ddbjgss124.seq 90748 80006096 299001174 ddbjgss125.seq 100558 80239342 299001811 ddbjgss126.seq 100057 69801629 299002227 ddbjgss127.seq 100725 68947184 299000110 ddbjgss128.seq 100696 69070924 299000397 ddbjgss129.seq 101127 69858329 299000445 ddbjgss130.seq 108267 73491017 299001110 ddbjgss131.seq 85948 71757452 299003119 ddbjgss132.seq 96687 75958163 299001980 ddbjgss133.seq 97735 87661799 299002528 ddbjgss134.seq 99077 66513684 299002133 ddbjgss135.seq 115982 74007797 299000094 ddbjgss136.seq 119165 74488510 299000208 ddbjgss137.seq 35071 21172794 92603798 ddbjhtc1.seq 42093 65471712 299004777 ddbjhtc2.seq 33890 75582416 299006863 ddbjhtc3.seq 33238 80491576 299000987 ddbjhtc4.seq 81475 51725347 299003043 ddbjhtc5.seq 87526 84453352 299003406 ddbjhtc6.seq 79820 94298753 299002027 ddbjhtc7.seq 77541 79908607 299001840 ddbjhtc8.seq 953 857533 2988002 ddbjhtg1.seq 1565 225473555 299011669 ddbjhtg2.seq 3362 221524874 299172498 ddbjhtg3.seq 3038 223597585 299007049 ddbjhtg4.seq 1896 223358825 299042273 ddbjhtg5.seq 1521 221473014 299030140 ddbjhtg6.seq 1500 221752872 299232102 ddbjhtg7.seq 1538 221335563 299230569 ddbjhtg8.seq 1333 225419722 299021454 ddbjhtg9.seq 1751 218901630 299265802 ddbjhtg10.seq 1141 229045780 299292949 ddbjhtg11.seq 898 230132394 299313501 ddbjhtg12.seq 888 229928502 299201015 ddbjhtg13.seq 967 229840436 299242452 ddbjhtg14.seq 921 229968388 299276622 ddbjhtg15.seq 2131 209864701 299002866 ddbjhtg16.seq 1384 222867555 299012093 ddbjhtg17.seq 1030 228228227 299001930 ddbjhtg18.seq 1031 228565782 299354870 ddbjhtg19.seq 1059 228411876 299237365 ddbjhtg20.seq 1002 228471747 299105352 ddbjhtg21.seq 926 229668955 299072414 ddbjhtg22.seq 1029 228749807 299180502 ddbjhtg23.seq 1095 227820214 299102391 ddbjhtg24.seq 1096 227916667 299207900 ddbjhtg25.seq 1106 227887686 299064524 ddbjhtg26.seq 1040 228790853 299197537 ddbjhtg27.seq 1131 227173471 299088566 ddbjhtg28.seq 1062 228535974 299188707 ddbjhtg29.seq 988 229498987 299217998 ddbjhtg30.seq 1047 228584143 299121251 ddbjhtg31.seq 1136 227844918 299274531 ddbjhtg32.seq 1117 227719475 299118049 ddbjhtg33.seq 1258 226408637 299088938 ddbjhtg34.seq 1356 224547442 299019124 ddbjhtg35.seq 1611 223544433 299148982 ddbjhtg36.seq 1385 224184967 299135813 ddbjhtg37.seq 1334 228760258 299007354 ddbjhtg38.seq 1505 228071012 299121315 ddbjhtg39.seq 1400 228933124 299051482 ddbjhtg40.seq 1331 228736062 299288110 ddbjhtg41.seq 1194 227344493 299040510 ddbjhtg42.seq 1232 226640165 299141571 ddbjhtg43.seq 1113 227031545 299292372 ddbjhtg44.seq 1250 226893680 299233353 ddbjhtg45.seq 1136 227001603 299104169 ddbjhtg46.seq 1182 226314356 299201286 ddbjhtg47.seq 1112 226148776 299053879 ddbjhtg48.seq 1315 225562264 299053352 ddbjhtg49.seq 1167 226690838 299144068 ddbjhtg50.seq 1347 222704104 299038701 ddbjhtg51.seq 1244 225836985 299168963 ddbjhtg52.seq 1241 226524859 299299548 ddbjhtg53.seq 1177 226029486 299090644 ddbjhtg54.seq 1501 225043792 299098406 ddbjhtg55.seq 1417 224159164 299191433 ddbjhtg56.seq 1517 221439264 299072150 ddbjhtg57.seq 1484 220859427 299139609 ddbjhtg58.seq 1510 220673604 299009101 ddbjhtg59.seq 1511 222460273 299092539 ddbjhtg60.seq 1526 228879890 299123396 ddbjhtg61.seq 1338 227643142 299058694 ddbjhtg62.seq 1765 228993087 299284177 ddbjhtg63.seq 1184 231800442 299158268 ddbjhtg64.seq 1234 231787259 299160814 ddbjhtg65.seq 1005 216509533 299017405 ddbjhtg66.seq 1294 200344154 259604997 ddbjhum1.seq 15184 189028424 299028743 ddbjhum2.seq 1657 214020202 299182799 ddbjhum3.seq 1620 223161453 299122144 ddbjhum4.seq 1416 216718706 299083096 ddbjhum5.seq 1467 215004303 299119481 ddbjhum6.seq 1486 213724912 299178765 ddbjhum7.seq 1564 208680289 299315304 ddbjhum8.seq 1682 216797193 299173772 ddbjhum9.seq 1561 213707207 299031679 ddbjhum10.seq 1843 214349062 299014648 ddbjhum11.seq 1935 213643174 299025879 ddbjhum12.seq 37771 161638509 299009521 ddbjhum13.seq 69103 96643147 299002710 ddbjhum14.seq 16838 177100068 299024243 ddbjhum15.seq 2787 220077995 299071278 ddbjhum16.seq 2071 222910938 299191960 ddbjhum17.seq 2497 220590062 299007269 ddbjhum18.seq 4580 215273796 299098708 ddbjhum19.seq 3103 211385021 299000799 ddbjhum20.seq 55485 99967650 299002794 ddbjhum21.seq 34296 112690438 299037681 ddbjhum22.seq 67721 116300979 299001184 ddbjhum23.seq 12630 43913093 81011069 ddbjinv1.seq 18397 195056449 299158884 ddbjinv2.seq 1113 195614178 299235976 ddbjinv3.seq 75954 100589051 299001015 ddbjinv4.seq 72842 101114518 299002611 ddbjinv5.seq 94845 86022863 299001588 ddbjinv6.seq 73586 102326541 299058423 ddbjinv7.seq 16175 71678020 149695914 ddbjmam1.seq 66098 130179398 299002158 ddbjmam2.seq 26174 50145303 124302073 ddbjpat1.seq 253014 87770034 299000052 ddbjpat2.seq 212254 101235929 299000934 ddbjpat3.seq 178455 122694288 299018754 ddbjpat4.seq 180577 107516832 299004354 ddbjpat5.seq 165875 98911998 299013892 ddbjpat6.seq 138970 124591065 299000333 ddbjpat7.seq 149253 111133789 299000647 ddbjpat8.seq 168296 98566392 299000773 ddbjpat9.seq 155396 61149398 298999944 ddbjpat10.seq 115188 71732339 299000813 ddbjpat11.seq 138209 62398415 299000231 ddbjpat12.seq 140415 69126653 299000975 ddbjpat13.seq 166864 63252988 299000841 ddbjpat14.seq 183386 81287957 299000448 ddbjpat15.seq 124865 135884831 299000748 ddbjpat16.seq 122269 132756218 299000497 ddbjpat17.seq 155991 105782736 299001684 ddbjpat18.seq 122012 103163606 299001047 ddbjpat19.seq 112971 101079868 299001665 ddbjpat20.seq 132433 51712360 215650391 ddbjphg.seq 2891 18960254 46437165 ddbjpln1.seq 37505 149317060 299011661 ddbjpln2.seq 1668 215069856 299118925 ddbjpln3.seq 34924 153783560 299002570 ddbjpln4.seq 90075 92721033 299091382 ddbjpln5.seq 71397 76137286 299006865 ddbjpln6.seq 32601 95158875 299085276 ddbjpln7.seq 3689 198802421 299023094 ddbjpln8.seq 1794 204226950 299892560 ddbjpln9.seq 63 236754414 309355695 ddbjpln10.seq 24995 183297196 299000348 ddbjpln11.seq 84806 86653696 299000218 ddbjpln12.seq 90646 92383180 299000229 ddbjpln13.seq 41373 137039582 299000994 ddbjpln14.seq 63855 101821322 278666402 ddbjpri1.seq 8383 212547613 299132696 ddbjpri2.seq 33303 145300580 250734965 ddbjrod1.seq 10358 203310773 299129173 ddbjrod2.seq 1107 207246389 299107336 ddbjrod3.seq 1072 207916873 299069631 ddbjrod4.seq 1109 208443295 299185286 ddbjrod5.seq 1164 215035651 299066412 ddbjrod6.seq 1164 215390657 299191603 ddbjrod7.seq 1189 217667319 299209309 ddbjrod8.seq 1185 217902487 299068055 ddbjrod9.seq 1225 221567726 299001894 ddbjrod10.seq 1154 220819524 299041346 ddbjrod11.seq 1206 221545458 299014669 ddbjrod12.seq 1142 217627342 299169778 ddbjrod13.seq 1162 221163599 299276035 ddbjrod14.seq 30684 176316853 299188666 ddbjrod15.seq 6722 216156830 299068311 ddbjrod16.seq 1450 231587399 299220125 ddbjrod17.seq 23192 194227734 299001729 ddbjrod18.seq 35730 97714971 299090411 ddbjrod19.seq 27218 188098346 299001562 ddbjrod20.seq 14174 17317511 53800315 ddbjsts1.seq 97030 44519781 299001086 ddbjsts2.seq 95573 48280675 299001509 ddbjsts3.seq 96206 40331452 299001568 ddbjsts4.seq 64651 38044996 299003188 ddbjsts5.seq 64932 37775860 299003369 ddbjsts6.seq 64680 38094396 299000113 ddbjsts7.seq 66634 45746067 299001559 ddbjsts8.seq 68566 52571652 299001672 ddbjsts9.seq 68575 52180586 299002133 ddbjsts10.seq 74541 49333500 299001325 ddbjsts11.seq 102028 42781021 299001647 ddbjsts12.seq 17284 5846239 40717205 ddbjsyn.seq 25784 37078074 115395325 ddbjuna.seq 205 111605 420884 ddbjvrl1.seq 85992 77132729 299000286 ddbjvrl2.seq 84746 77211006 299005238 ddbjvrl3.seq 83073 80617613 299002201 ddbjvrl4.seq 80721 83604710 298999994 ddbjvrl5.seq 6319 4760325 19869178 ddbjvrt1.seq 60009 138247168 299000827 ddbjvrt2.seq 26264 187425659 299175596 ddbjvrt3.seq 92761 85320785 299001711 ddbjvrt4.seq 26088 127921762 299001825 ddbjvrt5.seq 1477 231250235 299079370 ddbjvrt6.seq 1574 230843359 299114765 ddbjvrt7.seq 17628 206024517 299192839 ddbjvrt8.seq 35911 177431468 299003237 ddbjvrt9.seq 10428 10026978 34225960 ------------------------------------------------------------------------------ Total 55890995 60564721635 216628683992 ddbjcon.seq 511595 0 1150041875 ddbjtpa.seq 4858 15861858 35379762 The entries and bases in the CON division and TPA dataset are not counted in the numbers given on the top of the release note or 'Total' on the above table.