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Nucleic acid database
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- 3. Aims: • Need forstoring and communicating large datasets has grown. • Make biological data available to scientists. • To make biological data available in computer-readable form. • To enhance availability.
- 4. Classification of database: Primary database Composite database Secondary database
- 5. Forms: • Technical design •Flat-files • Relational database (SQL) • Exchange/publication technologies (FTP, HTML, CORBA, XML,...)
- 7. Availablity: • Publicly available,no restrictions • Available, but with copyright • Accessible, but not downloadable • Academic, but not freely available • Proprietary, commercial; possibly free for academics
- 8. Terminology: • LOCUS – sizeof sequence (in base pairs) – nature of molecule (e.g. DNA or RNA) – topology (linear or circular) • DEFINITION: brief description of gene • ACCESSION: unique identifier for this (and some other) databases • VERSION: lists synonymous or past ID numbers
- 9. Terminology: • KEYWORDS: listof terms related to entry; can be used for keyword searching for related data • SOURCE: common name of relevant organism • ORGANISM: complete id, with taxonomic classification
- 10. Terminology: • REFERENCE: creditsauthor(s) who initially determined the sequence; includes subsections: – AUTHOR – TITLE – JOURNAL – PUBMED • COMMENT: free-formatted text that doesn’t fit in another category
- 11. Primary nucleotide sequence databases •EMBL www.ebi.ac.uk/embl/ • GenBank www.ncbi.nlm.nih.gov/Genbank/ • DDBJ www.ddbj.nig.ac.jp
- 12. Genbank • An annotatedcollection of all publicly available nucleotide and proteins • Set up in 1979 at the LANL (Los Alamos). • Maintained since 1992 NCBI (Bethesda). • http://www.ncbi.nlm.nih.gov
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- 14. EMBL Nucleotide SequenceDatabase • An annotated collection of all publicly available nucleotide and protein sequences • Created in 1980 at the European Molecular Biology Laboratory in Heidelberg. • Maintained since 1994 by EBI- Cambridge. • http://www.ebi.ac.uk/embl.html
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- 16. DDBJ–DNA Data Bankof Japan • An annotated collection of all publicly available nucleotide and protein sequences • Started, 1984 at the National Institute of Genetics (NIG) in Mishima. • Still maintained in this institute a team led by Takashi Gojobori. • http://www.ddbj.nig.ac.jp
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- 18. Derived databases • CUTGCodon usage tabulated from GenBank http://www.kazusa.or.jp/codon/ • Genetic Codes Deviations from the standard genetic code in various organisms and organelles http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mo de=c • TIGR Gene Indices Organism-specific databases of EST and gene sequences http://www.tigr.org/tdb/tgi.shtml • UniGene Unified clusters of ESTs and full-length mRNA sequences http://www.ncbi.nlm.nih.gov/UniGene/ • ASAP Alternative spliced isoforms http://www.bioinformatics.ucla.edu/ASAP • Intronerator Introns and alternative splicing in C.elegans and C.briggsae http://www.cse.ucsc.edu/~kent/intronerator/
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- 25. Nucleic acid structure databases •NDB Nucleic acid-containing structures http://ndbserver.rutgers.edu/ • NTDB Thermodynamic data for nucleic acids http://ntdb.chem.cuhk.edu.hk/ • RNABase RNA-containing structures from PDB and NDB http://www.rnabase.org/ • SCOR Structural classification of RNA: RNA motifs by structure, function and tertiary interactions • http://scor.lbl.gov/ 7/14/2020 5:50 PM
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- 30. Sequence Retrieval Tools •Various tools to get sequences of interests from databases • Entrez in NCBI http://www.ncbi.nlm.nih.gov/Entrez • SRS for EMBL and other DBs http://srs.ebi.ac.uk • Fetch in GCG package • Seqret in EMBOSS
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