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Practical 1 Exploring Bioinformatics Resources (Biological Databases)

Practical 1 Exploring Bioinformatics Resources (Biological Databases). Biological databases. Structured storage of many kinds of data, including: Sequence (eg chromosomal DNA, mRNA, protein) Structures Literature (eg PubMed) Diseases Biomolecular interactions Etc etc etc etc.

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Practical 1 Exploring Bioinformatics Resources (Biological Databases)

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  1. Practical 1 Exploring Bioinformatics Resources (Biological Databases)

  2. Biological databases • Structured storage of many kinds of data, including: • Sequence (eg chromosomal DNA, mRNA, protein) • Structures • Literature (eg PubMed) • Diseases • Biomolecular interactions • Etc etc etc etc

  3. Databases, continued: • Databases can come and go. • There can be: • Multiple databases for a single kind of data (eg protein sequence, pathways, etc) • New databases for “new” kinds of data • Every database has its own peculiarities And so….

  4. A good biologist • Acquires a general set of skills for FINDING and USING databases • “poke around” • “look” • “think” • Can critically assess the contents of databases

  5. P1: a gentle introduction to databases LEARNING GOALS: • Know how to perform simple queries of several databases • Gain some familiarity with the contents of selected databases • Learn to identify distinct elements of database records • Use database cross references to link to other databases • Know multiple approaches to find biological data on the internet

  6. The exercise • Take an introductory look at selected databases • Find additional databases using the Nucleic Acids Research Database Issue

  7. Section A: An introductory look at biological databases Follow the instructions in the exercise to look at: • Protein: database of protein sequences • Gene: Whole genome annotation • OMIM: genes and diseases • KEGG Pathway: metabolic and signalling pathways • PDB: three-dimensional biomolecular structures

  8. Section B: the Nucleic Acids Research database issue – identifying useful databases • Hundreds of DBs out there, and more coming all the time • Various ways to find them:  Google etc  PubMed (eg p53 database)  Catalogs of the databases

  9. NAR Database Categories List From: http://nar.oxfordjournals.org/content/39/suppl_1/D1/suppl/DC1 Investigate databases in the NAR Database Categories list

  10. Nucleic Acids Research Database Issue • Special supplementary issue of the Nucleic Acids Research journal • Collection of all DBs published in NAR & selected DBs relevant to biologists • not complete, but contains most of the popular DBs • Hotlinks & brief summaries provided for each DB • Catalog List: Categorize the DBs based on different type of info • E.g., sequence, structure, signaling, plant, metabolics, disease From: http://nar.oxfordjournals.org/content/41/D1/D1/suppl/DC1

  11. Capture your answers Eg: • Capture your answers electronically by writing them in the exercise Ms Word document provide for each practical  Start a new Word document or Excel document… You work will be discussed before the end of the practical

  12. Begin your exercise work now

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