Department of Botany Mangaldai College Mangaldai EMail pdekamldgmailcom Bioinformatics Biologists Collect Molecular Data DNA amp Protein Sequences Gene Expression etc Computer scientists ID: 1045584
Download Presentation The PPT/PDF document "Dr. Prativa Deka Associate Professor" is the property of its rightful owner. Permission is granted to download and print the materials on this web site for personal, non-commercial use only, and to display it on your personal computer provided you do not modify the materials and that you retain all copyright notices contained in the materials. By downloading content from our website, you accept the terms of this agreement.
1. Dr. Prativa DekaAssociate ProfessorDepartment of BotanyMangaldai College, MangaldaiE-Mail: pdeka.mld@gmail.comBioinformatics
2. Biologists Collect Molecular Data: DNA & Protein Sequences,Gene Expression, etc.Computer scientists (+Mathematicians, Statisticians, etc.)Develop Tools, Softwares, Algorithms to Store and Analyze the Data.BioinformaticiansStudy of Biological Questions by Analyzing Molecular DataBioinformatics: The field of science in which biology, computer science and information technology merge into a single discipline Paulien hogeweg
3. From DNA to Genome3Watson and Crick DNA modelSanger sequences insulin proteinSanger dideoxy DNA sequencingPCR (Polymerase Chain Reaction)1955196019651970197519801985ARPANET (early Internet)PDB (Protein Data Bank)Sequence alignmentGenBank databaseDayhoff’s Atlas
4. 4199519902000SWISS-PROT databaseNCBIWorld Wide WebBLASTFASTAEBIHuman Genome InitiativeFirst human genome draftFirst bacterial genomeYeast genome
5. Biological Databases What is a database?A collection of related data elementstablescolumns (fields)rows (records)Records retrieved using a query languageDatabase technology is well established11/15/20175
6. Tables (entitites)basic elements of information to track, e.g., gene, organism, sequence, citationColumns (fields)attributes of tables, e.g. for citation table, title, journal, volume, author Rows (records)actual datawhereas fields describe what data is stored, the rows of a table are where the actual data is stored11/15/20176
7. How online database work?11/15/20177When you query an online database, your query is translated into SQL, the database is interrogated, and the answer displayed on your web browser. Your computer and browser (the “client”)Software to receive and translate the instructions you enter into your browser (on the “server”)The database itselfImage source: David Lane and Hugh E. Williams. Web Database Applications with PHP & MySQL. O’Reilly (2002).
8. Why biological databases?Make biological data available to scientistsConsolidation of data (gather data from different sources)Provide access to large dataset that cannot be published explicitly (genome, proteome,…)Make biological data available in computer-readable formatMake data accessible for automated analysisBioinformatics: “To extract, store and to analysis the biological data”
9. Biological DatabasesOver 1000 biological databasesVary in size, quality, coverage, level of interestMany of the major ones covered in the annual Database Issue of Nucleic Acids ResearchWhat makes a good database?comprehensivenessaccuracyis up-to-dategood interfacebatch search/downloadAPI (web services, DAS, etc.)11/15/20179
10. Types of Biological Databases
11. Flow of Databases in BioinformaticsBiological experimentsBiological DatabasesComputational Biology
12. Plants Genomes DatabasesPlant Genomes Databases
13. Ten Important Bioinformatics DatabasesGenBank www.ncbi.nlm.nih.gov nucleotide sequencesEnsembl www.ensembl.org human/mouse/Plants genomePubMed www.ncbi.nlm.nih.gov literature referencesNR www.ncbi.nlm.nih.gov protein sequencesSWISS-PROT www.expasy.ch protein sequencesInterPro www.ebi.ac.uk protein domainsOMIM www.ncbi.nlm.nih.gov genetic diseasesEnzymes www.chem.qmul.ac.uk enzymesPDB www.rcsb.org/pdb/ protein structuresKEGG www.genome.ad.jp metabolic pathwaysIn 1965, Dayhoff gathered all the available sequence data to create the first bioinformatics database (Atlas of Protein Sequence and Structure).
14. NCBI (National Center for Biotechnology Information)over 30 databases including GenBank, PubMed, OMIM, and GEO Access all NCBI resources via Entrez (www.ncbi.nlm.nih.gov/Entrez/)
15.
16. Protein Data Bank (PDB)
17. BLAST For Sequence AlignmentBasic Local Alignment Search ToolAltschul et al. 1990,1994,1997A best method for local alignment Designed specifically for database searchesBenefits-Speed, User friendly, Statistical rigor,More sensitive Types of BLAST- BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX
18. Luscombe, Greenbaum, Gerstein (2001)
19. THANK YOU