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DDBJ, Bilogical Data Bases, Bioinformatics Data Base

The DNA Data Bank of Japan (DDBJ) is the sole nucleotide sequence data bank in Asia that collects nucleotide sequences from researchers and issues internationally recognized accession numbers. It exchanges data daily with similar databases in Europe and the US to maintain virtually identical, unified sequence data. DDBJ collects experimentally determined nucleotide sequence data and genomic data from various patent offices according to agreed-upon rules. Its goal is to improve the quality of the International Nucleotide Sequence Database.

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262 views2 pages

DDBJ, Bilogical Data Bases, Bioinformatics Data Base

The DNA Data Bank of Japan (DDBJ) is the sole nucleotide sequence data bank in Asia that collects nucleotide sequences from researchers and issues internationally recognized accession numbers. It exchanges data daily with similar databases in Europe and the US to maintain virtually identical, unified sequence data. DDBJ collects experimentally determined nucleotide sequence data and genomic data from various patent offices according to agreed-upon rules. Its goal is to improve the quality of the International Nucleotide Sequence Database.

Uploaded by

Rajesh Guru
Copyright
© Attribution Non-Commercial (BY-NC)
We take content rights seriously. If you suspect this is your content, claim it here.
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DNA Data Bank of Japan (DDBJ)

DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) is the sole nucleotide sequence data bank in Asia, which is officially certified to collect nucleotide sequences from researchers and to issue the internationally recognized accession number to data submitters. It exchange the collected data with EMBL-Bank/EBI (European Bioinformatics Institute) and GenBank/NCBI (National Center for Biotechnology Information) on a daily basis, the three data banks share virtually the same data at any given time. DDBJ/EMBL-Bank/GenBank collects
the nucleotide sequence data experimentally determined, and constructs the database in accordance with the rule agreed with the three databanks. The database also includes the data from Japan Patent Office (JPO), European Patent Office (EPO), United States Patent and Trademark Office (USPTO), and Korean Intellectual Property Office (KIPO). DDBJ is organized by CIB-DDBJ; Center for Information Biology and DNA Data Bank of Japan of NIG; National Institute of Genetics with endorsement of MEXT; Japanese Ministry of Education, Culture, Sports, Science and Technology. The principal purpose of DDBJ operations is to improve the quality of INSD, as public domains.The

virtually unified database is called "the International Nucleotide Sequence Database (INSD)". DDBJ collects sequence data mainly from Japanese researchers, but of course accepts data and issue the accession number to researchers in any other countries. Data Searching done by Data retrieval by accession numbers (getentry), All-round Retrieval of
Sequence and Annotation (ARSA), Retrieval of unified taxonomy database(TXSEARCH), DDBJ Vector Screening System & Blast. Genome analysis is done by Genome information broker(GIB), GIB for Viruses (GIB-V), Reannotation of bacterial genomes using a new common protocol (GTPS), Genome to protein structure and function (GTOP)

DDBJ recommend using Mass Submission System (MSS) when:


the submission consists of large number of sequences. the complex submission containing many features (more than 30). the submission with long sequences. the submission is not applicable for SAKURA, i.e. submissions of WGS or MGA (Mass sequence for genome annotation)

SAKURA is an interactive application for nucleotide sequence submission to enter all of items required for your submission on step by step basis. When the submission contents are not so many, SAKURA is very useful, an easy procedure for your submission. However, in case of large scale submission, such as thousands of ESTs, it is more useful to send submission files directly to DDBJ, rather than SAKURA. The accession number assigned to each of MGA entries is composed of 12 letters (five alphabetical characters and seven numeric numbers). The detail of accession number is shown as follows; Example:ZZZZZ0000001, (5 alphabetical characters -- project identifier./ first two characters -- identifier to each project./ third to fifth characters -- identifier to each of resources on each project./ 7 digit numeric numbers -- number for each sequence entry in a resource.) The accession number assigned to each WGS data consists of 4 letters + 8 (sometimes 9 or 10, if necessary) digits.Example:ZZZZ01000001/4 letters - Prefix to distinguish eachproject/ 2 digits -- Version number of the data set 6 digits -- ID of each individual sequence (It sometimes be 7 or 8 digits according to the number of entries.)

FORMAT FOR DDBJ


LOCUS 2003 DEFINITION ACCESSION VERSION KEYWORDS SOURCE ORGANISM AB123456 563 bp DNA linear BCT 23-OCT-

Verrucosispora sp. 431C09 gene for 16S rRNA, partial sequence. AB123456 AB123456.1 . Verrucosispora sp. 431C09 Verrucosispora sp. 431C09 Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Micromonosporineae; Micromonosporaceae; Verrucosispora. REFERENCE 1 (bases 1 to 563) AUTHORS Muramatsu,H., Shahab,N.B., Tsurumi,Y. and Hino,M. TITLE Direct Submission JOURNAL Submitted (15-OCT-2003) to the DDBJ/EMBL/GenBank databases. Contact:Hideyuki Muramatsu Fujisawa Pharmaceutical Co., Ltd., Exploratory Research Laboratories; Tokodai 5-2-3, Tsukuba, Ibaraki 300-2698, Japan REFERENCE 2 AUTHORS Muramatsu,H., Shahab,N., Tsurumi,Y. and Hino,M. TITLE A comparative study between Malaysian and Japanese actinomycetes JOURNAL Unpublished (2003) COMMENT FEATURES Location/Qualifiers source 1..563 /db_xref="taxon:250264" /mol_type="genomic DNA" /note="Malaysian soil actinomycetes" /organism="Verrucosispora sp. 431C09" /strain="431C09" rRNA <1..>563 /product="16S rRNA" BASE COUNT 120 a 140 c 205 g 98 t ORIGIN 1 gagcggcgaa cgggtgagta acacgtgagc aacctgccct aggctttggg ataaccctcg 61 gaaacggggg ctaataccga ataggacctc ctgtcgcatg gtggggggtg gaaagttttt 121 cggcctggga tgggctcgcg gcctatcagc ttgttggtgg ggtgatggcc taccaaggcg 181 acgacgggta gccggcctga gagggcgacc ggccacactg ggactgagac acggcccaga 241 ctcctacggg aggcagcagt ggggaatatt gcacaatggg cggaagcctg atgcagcgac 301 gccgcgtgag ggatgacggc cttcgggttg taaacctctt tcagcaggga cgaagcgcaa 361 gtgacggtac ctgcagaaga agcgccggcc aactacgtgc cagcagccgc ggtaagacgt 421 agggcgcgag cgttgtccgg atttattggg cgtaaagagc tcgtaggcgg cttgtcgcgt 481 cgactgtgaa aacccgcagc tcaactgcgg gcctgcagtc gatacgggca ggctagagtt 541 cggtagggga gactggaatt cct //

REF:- http://www.ncbi.nlm.nih.gov/collab/FT/

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