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biological detabase

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  • 1. . Biological Databses Presented By: Bhakti Thakkar M.L.I.Sc 2012-13
  • 2. *A database is a collection ofinformation that is organizedso that it can easily beaccessed, managed, andupdated. *
  • 3. *Harrod’s Librarien’s Glossary defines, “Database as any grouping of data for a particular purpose or for the use of a particular set of end users, usually organized via fields and providing tools to enable manipulation of the data such as sorting, grouping, extraction and reporting”. *
  • 4. Types of Databases Source databaseReference database contains references or contains citations Informative text, raw data *
  • 5. Biological Databses Biogrid database Rfam database Mir base database Modbase database
  • 6. * The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein and genetic interactions.* It wascreated in 2003 by Mike Tyers, Bobby-Joe Breitkreutz, and Chris Stark at the Samuel Lunenfeld Research Institute at Mount Sinai Hospital.* It strives to provide a comprehensive resource of protein–protein and genetic interactions for all major model organism species *
  • 7. *BiOGRID searches can be performed by clicking on the “gene” tab from the main search page.* To perform search, one can simply enter term and search engine will search for matching identifiers.*Advanced search option can be also used for the better results. *
  • 8. Search options at BioGRID Wildcard Searches Publication Searches *
  • 9. * The BioGRID supports wildcard searching (ie. searching where the search is not exact but rather a range of possible matches) on the TAIL end of any keyword entered in our search field.* To perform a wildcard search, simply enter your prefix (must be 3 letters or more) followed by a star (*).* Examples: STE*, CDC*, YAL01*, CLN* *
  • 10. *Publication searches help tosearch using publications likejournals, magazines, aritcalsetc. *
  • 11. *Rfam is an open access database, hosted at the Wellcome Trust Sanger Institute, containing information about RNA(Ribonucleic acid) families.*Rfam contains information for RNA families and annotations for millions of RNA genes. *
  • 12. Rfam Database Search Batch Sequence sequenceKeyword Taxonomy Entry Type *
  • 13. * To Find Rfam families within your sequence of interest use Sequence search* To find multiple sequences to be searched for matching Rfam families use Batch sequence* To search for keywords within the textual data in the Rfam database use Keyword search* For a complex expression that precisely defines the species distribution of families use Taxonomy search* for Search for Rfam families by type like Gene, anti- toxin etc. use Entry Type search *
  • 14. * miRBase is a biological database that acts as an archive of microRNA sequences and annotations.* The miRBase registry provides a centralised system for assigning new names to microRNA genes.* The miRBase Sequence database is the primary repository for published microRNA (miRNA) sequence and annotation data. * Database
  • 15. *
  • 16. miRBase has five aims: To provide a consistent naming system for microRNAs To provide a central place collecting all known microRNA sequences To provide human and computer readable information for each microRNA To provide primary evidence for each microRNA To aggregate and link to microRNA target information
  • 17. MiRBase database search features By miRNA identifier or keyword By genomic location For clusters By tissue expression By sequence
  • 18. miRBase provides the following services: The miRBase database is a searchable database of published miRNA sequences and annotation Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. The miRBase Registry provides miRNA gene hunters with unique names for novel miRNA genes prior to publication of results.
  • 19. Modbase detabase MODBASE is a query able database of annotated protein structure models. MODBASE contains theoretically calculated models, which may contain significant errors, not experimentally determined structures..
  • 20. Modbase detabaseModBase Search : ModBase is a database of comparative protein structure models,calculated by our modeling pipeline ModPipe.ModBase Search Search type model (default) Sequence similarity (blast) Display type:- model detail, model overview, sequence overview. Search by properties. Database accession number Annotation keywords Gene name
  • 21. Advance Search option Internal id Template pdb code Template or homolog pdb codeOrganism:- Homoslapiens Mas musculus and allIn advance search :- Select property options:- Model size, E-value (0-100) Model score (0-100) Protein size % seq. lent (0-100) Minimum and maximum Search-(and, or) Apply to-all models of sequence, some models of a sequence Hide advanced properties.
  • 22. Modbase provides the following services: MODBASE uses the MySQL relational database management system for flexible querying and CHIMERA for viewing the sequences and structures (http://www.cgl.ucsf.edu/chimera/). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, as well as improvements in the software for calculating the models. The largest data set contains 1,26,629 models for domains in 659,495 out of 1,182,126 unique protein sequences in the complete Swiss-Prot/TrEMBL database (August 25, 2003); only models based on alignments with significant similarity scores and models assessed to have the correct fold despite insignificant alignments are included.
  • 23.  The 53 new structures produced by the consortium allowed us to characterize structurally 24,113 sequences. Our other resources associated with MODBASE include a comprehensive database of multiple protein structure alignments