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Introduction to Practical 1

Biological databases

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BIOINFORMATICS ~ biology + computers Data (databases) Query and Analysis of Data (software/tools)

….more on this in your upcoming lectures….

Overview of L1

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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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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….

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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

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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

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The exercise

Section A) Take an introductory look at selected databases

Section B) Find additional databases using the Nucleic Acids

Research Database Issue

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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

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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

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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

From: http://nar.oxfordjournals.org/content/39/suppl_1/D1/suppl/DC1

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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

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Begin your exercise work now