Notes on Nucleotide Sequence Databases

Nucleotide sequence database contain sequence data of DNA, cDNA, mRNA and tRNA
•Sequences always listed form 5’-3’ direction
•Sequences are present as same as in vivo
•cDNA sequences are considered as RNA sequences

EMBL, GenBank, and DDBJ are the three primary nucleotide sequence databases
•EMBL www.ebi.ac.uk/embl/
•GenBank www.ncbi.nlm.nih.gov/Genbank/
•DDBJ www.ddbj.nig.ac.jp

1. Genbank (Genetic Sequence Data bank)
•An annotated collection of all publicly available nucleotide and protein sequence maintained by NCBI (National Center For Biotechnology Information)
•NCBI estd in 1988 at National Institute of Health (NIH), Maryland, USA
•Maintained since 1992 NCBI (Bethesda).
•http://www.ncbi.nlm.nih.gov
•Entrez: integrated biological database retrieval system
Sequence Submission tools:
1.BankIt
•web based Sequence Submission tools
•Submission of a single sequence, large number of sequences or few unrelated sequences with many features
•Provide option to user to update an existing record
2. Seqin:
•enable submission and updation to Genbank
•Can handle simple as well as complex long sequences

2. EMBL/EBI Nucleotide Sequence Database
European Molecular Biology Laboratory/European Bioinformatics Institute

•An annotated collection of all publicly available DNA and RNA sequences
•Created in 1980 at the European Molecular Biology Laboratory in Heidelberg, Germany
•Worlds first nucléotide séquence data base
•Works in collaboration with Genbank and DDBJ (International nucleotide sequence database collaboration, INSDC)
•Maintained since 1994 by EBI- Cambridge.
•http://www.ebi.ac.uk/embl.html
•Sequence retrieval system (SRS): used to retrieve biological data
Webin: internet based sequence submission system used to submit single or large sequences or also to update already existing sequences
•Accession no: unique sequence identifier that helps identification of submitted sequences
•BLAST2EVEC: algorithm to screen the submitted sequence for vector contamination
•Sequence analysis tools: Align, Clustal W2, DNA block aligner(DBA) etc

3. DDBJ–DNA Data Bank of Japan
•An annotated collection of all publicly available nucleotide sequences
•DNA Data Bank of Japan is the sole nucleotide sequence data bank in Asia
•Started, 1984 at the National Institute of Genetics (NIG) in Mishima.
•Part of INSDC
•Still maintained in this institute a team led by Takashi Gojobori.
•http://www.ddbj.nig.ac.jp
•Submission tools
     (A) Nucleotide Sequence Submission System or SAKURA that allows user to submit nuccleotide sequences, translated amino acid sequences , their features and functions.
       (B) Mass Submission System (MSS)-used to submit complex sequences, long sequences or large number of sequences