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Biological databases

Biological databases. Nicky Mulder: nicola.mulder@uct.ac.za. What is a database. an organized body of related infomation www.cogsci.princeton.edu/cgi-bin/webwn Data collection that is: Structured (computer readable) Searchable Updatable Cross-linked Publicly available.

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Biological databases

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  1. Biological databases Nicky Mulder: nicola.mulder@uct.ac.za

  2. What is a database • an organized body of related infomation www.cogsci.princeton.edu/cgi-bin/webwn • Data collection that is: • Structured (computer readable) • Searchable • Updatable • Cross-linked • Publicly available

  3. Biological Databases • Make data available to public • So much data available, needs ordering • Turn data into computer-readable form • Ability to retrieve data from various sources • Can have primary (archival) or secondary databases (curated) Most commonly used are sequence databases

  4. Biological systems Sequence data Protein folding and 3D structure Taxonomic data Literature Pathways and networks Protein families and domains Small molecules Whole genome data Biological systems

  5. Biological systems Sequence data Protein folding and 3D structure Taxonomic data Literature Pathways and networks Protein families and domains Small molecules Whole genome data Biological systems

  6. Biological systems Sequence data Protein folding and 3D structure Taxonomic data Literature Pathways and networks Protein families and domains Small molecules Whole genome data Ontologies -GO Biological systems

  7. Sequence databases • Used for retrieving a known gene/protein sequence • Useful for finding information on a gene/protein • Can find out how many genes are available for a given organism • Can comparing your sequence to the others in the database • Can submit your sequence to store with the rest • Main databases: nucleotide and protein sequence DBs

  8. Requirements for good sequence database • It must be complete with minimal redundancy • It must contain as much up-to-date information (annotation) as possible on each sequence • All the information items must be retrievable by computer programs in a consistent manner • It must be highly interoperable with other databases

  9. Nucleotide sequence databases Exons • EMBL, DDBJ, GenBank • Data submitted by sequence owner • Must provide certain information and CDS if applicable • No additional annotation added • Entries never merged –some redundancy Promoter CDS (coding sequence)

  10. Accession number Example EMBL entry 1: general info ID AB083336 standard; genomic DNA; MAM; 6116 BP. AC AB083336; XX SV AB083336.1 DT 06-JAN-2005 (Rel. 82, Created) DT 06-JAN-2005 (Rel. 82, Last updated, Version 1) DE Sus scrofa p27Kip1 gene for p27Kip1, p27Kip1R, complete cds, alternative DE splicing. OS Sus scrofa (pig) OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Cetartiodactyla; Suina; Suidae; Sus. RN [1] RP 1-6116 RA Hirano K., Shintani Y., Hirano M., Kanaide H.; RT ; RL Submitted (08-APR-2002) to the EMBL/GenBank/DDBJ databases. RL Katsuya Hirano, Graduate School of Medical Sciences, Kyushu University, RL Division of Molecular Cardiology, Research Institute of Angiocardiology; RL 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka, 812-8582, Japan RL (E-mail:khirano@molcar.med.kyushu-u.ac.jp, Tel:81-92-642-5550, RL Fax:81-92-642-5552) RN [2] RA Shintani Y., Hirano K., Hirano M., Nishimura J., Nakano H., Kanaide H.; RT "Cloning and Charaterization of full sequence of porcine p27Kip1 gene and RT expression of splice isoform p27Kip1R"; RL Unpublished. Description of gene References

  11. Example EMBL entry 2:features on the sequence -CDS FH Key Location/Qualifiers FT source 1..6116 FT /db_xref="taxon:9823" FT /mol_type="genomic DNA" FT /organism="Sus scrofa" FT /cell_type="liver" FT /clone_lib="lambda Fix II porcine genomic DNA" FT exon 784..1714 FT /evidence=NOT_EXPERIMENTAL FT /note="The residue 2591 corresponds to the transcription FT initiation site determined in human gene" FT CDS join(1240..1714,2261..2271,5104..5160) FT /codon_start=1 FT /gene="p27Kip1" FT /product="p27Kip1R" FT /protein_id="BAD83612.1" FT /translation="MSNVRVSNGSPSLERMDARQAEYPKPSACRNLFGPVNHEELTRDL FT EKHCRDMEEASQRKWNFDFQNHKPLEGKYEWQEVEKGSLPEFYYRPPRPPKGACKVPAQ FT EGQGVSGTRQAVPLIGSQANSEDTHLVDQKTDAPDSQTGLAEQCTGIRKRPATDDSSPP FT SVSLKIGMYQLNYSSVW" Feature type and location Corresponding protein sequence Feature name and information

  12. Example EMBL entry 3:features on the sequence –introns and exons FT intron 1715..2260 FT /cons_splice=(5'site:NO,3'site:NO) FT exon 2261..2390 FT /number=2 FT intron 2391..4494 FT /cons_splice=(5'site:NO,3'site:NO) FT exon 4495..5824 FT /note="ending at a putative poly A site following a polyA FT signal" FT /number=3 FT polyA_signal 5802..5807 XX SQ Sequence 6116 BP; 1583 A; 1392 C; 1438 G; 1703 T; 0 other; gcggccgcga gctcaattaa ccctcactaa agggagtcga ctcgatctcg aagccctttt 60 cttgttttta ttgagggaga gcttgggttc agaatacatt acaaatgcag catctattcc 120 agtctactta tagaaagacg tcctcctggg cttcccccct aagccccctg cctcccctag 180 aacagcacag acttctaggt taagggtgag ctaaccactg ctcaccccca gctaaggcac 240 ccaggctcag gggctccccg cctcccccgc tgagcgagcg gtgggggccc ccccgggaga 300 gagcccagct gggggccgag cgcccagcgg cgagcccagc tgcccgcccc tacccgctcg 360 gcgagcgagg ggaaaataag atcgccctcg gcgaggagag ggaggtcggg gctccggagc 420 DNA sequence

  13. Summary of information in EMBL entries • Describes sequence type, e.g. genomic DNA, RNA, EST • Provides taxonomy from which sequence came • Provides information on submitters and references • Describes features on a sequence NB for function, replication, recombination, structure etc. • Shows if the DNA encodes a protein (CDS) and provides protein sequence • Provides actual nucleotide sequence

  14. DNA RNA Protein Protein cleavage Protein modification Ac S S Transported to organelle or membrane Folded into secondary or tertiary structure Performs a specific function Protein sequences All this info needs to be captured in a database

  15. Protein Sequence Databases • UniProt: • Swiss-Prot –manually curated, distinguishes between experimental and computationally derived annotation • TrEMBL - Automatic translation of EMBL, no manual curation, some automatic annotation • GenPept -GenBank translations • RefSeq - Non-redundant sequences for certain organisms • IPI –International protein Index –combination of many protein sequence databases

  16. Example of a Swiss-Prot entry 1 General information References

  17. Example of a Swiss-Prot entry 2 Functional information Cross-references

  18. Example of a Swiss-Prot entry 3 Keywords Features Sequence

  19. Swiss-Prot annotation mainly found in: • Description (DE) lines • Protein name/function • Comment (CC) lines • e.g. function, subcellular location, pathway, cofactor, disease, etc. • Feature table (FT) • features on the sequence, e.g. domain, active site, modifications, variations, etc. • Keyword (KW) lines • Set of a few hundred controlled vocabulary terms

  20. Other parts to UniProt • UniParc –archive of all sequences • UniProt –Swiss-Prot + TrEMBL • UniProt NREF100 (100% seqs merged) • UniProt NREF90 (90% seqs merged) • UniProt NREF50 (50% seqs merged)

  21. Submitting sequences to EMBL or UniProt WEB-IN -web-based submission tool for submitting DNA sequences to EMBL database. Protein sequences submitted when the peptides have been directly sequenced. Submit through SPIN

  22. Sequence formats • Not MSWord, but text! • Most include an ID/name/annotation of some sort • FASTA, E.g. >xyz some other comment ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcgctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgccagatcaaggctcatgtagcctcactgg Others specific to programs, e.g. GCG, abi, clustal, etc.

  23. Literature database: PubMed/Medline • Source of Medical-related & scientific literature • PubMed has articles published after 1965 • Can search by many different means, e.g. author, title, date, journal etc., or keywords for each • Can save queries and results • Can usually retrieve abstracts and full papers • PubMed has list of tags to search specific fields, e.g. [AU], [TI], [DP] etc.

  24. Search fields in PubMed • Title Words [TI]MeSH Terms [MH] • Title/Abstract Words [TIAB] Language [LA] • Text Words [TW] Journal Title [TA] • Substance Name [NM] Issue [IP] • Subset [SB] Filter [FILTER] • Secondary Source ID [SI] Entrez Date [EDAT] • Subheadings [SH] EC/RN Number [RN] • Publication Type [PT] Author Name [AU] • Publication Date [DP] All Fields [ALL] • Personal Name as Subject [PS] Affiliation [AD] • Page Number [PG]Unique Identifiers [UID] • Title Words [TI] MeSH Major Topic [MAJR] • MeSH Date [MHDA]

  25. Taxonomy Databases • Most used is NCBI’s taxonomy database: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Taxonomy • Provides entries for all known organisms • Provides taxonomic lineage and translation table for organisms • Sequence entries for organism • UniProt-specific taxonomy database is Newt: • http://www.ebi.ac.uk/newt

  26. Example taxonomy entry

  27. Where to find the databases • Table of addresses for major databases and tools • Nucleic Acids Research Database issue January each year • Nucleic Acids Research Software issue –new • Amos’s list of tools: http://www.expasy.ch/alinks.html

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