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Introduction to Practical 1 Biological databases 1 Overview of L1 BIOINFORMATICS ~ biology + computers Data (databases) Query and Analysis of Data (software/tools) ….more on this in your upcoming lectures…. 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 quality of a search (in terms of specificity, true positives (relevant hits) and false positives (irrelevant hits), as well as 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 Section A) Take an introductory look at selected databases Section B) 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 An example of a database catalogue: 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 • eg, sequence, structure, signaling, plant, metabolics, disease 10 From: http://nar.oxfordjournals.org/content/39/suppl_1/D1/suppl/DC1 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 11 Begin your exercise work now 12