BIOINFORMATICS
RESOURCES
a primer
A N DR EA MI L L E R -NESBI T T
L I A I SON L I BR A R IA N

AN DR EA .MI LL ER -NESBI T...
Objectives
By the end of this workshop you will be able to…
•
•
•
•
•

Understand differences between various bioinformati...
Bioinformatics is…
“…us[ing] computers to store, retrieve,
analyze or predict the composition or the
structure of biomolec...
http://www.ncbi.nlm.nih.gov/genbank/genbankstats-2008/
Applications of bioinformatics

http://deliverymatez.com/store/index.php?route=product/category&path=70, http://ftdtheothe...
Bioinformatics subject guide

http://www.mcgill.ca/library/find/subjects/health/bioinformatics
Freely available resources
http://www.ncbi.nlm.nih.gov/Database/datamodel/
Types of resources
Database vs Tool
Databases
•repositories of primary biological data
• Ex. GenBank

Tools
•manipulate or...
Types of resources
Uncurated vs Curated Databases
Uncurated
•Raw datasets with no annotation
• Ex. Nucleotide, Protein

Cu...
Let’s take a closer look…
Uncurated (GenBank)

Curated (RefSeq)

Author submits

NCBI creates record from existing data

O...
Results display
1.

Context—information about the sequence

2.

Features—annotation of the sequence
•

3.

Complete list o...
Activity!

http://www.camelcitydispatch.com/wp-content/uploads/2012/12/mad-scientist-movie1.jpg
Getting help
Questions?

Andrea Miller-Nesbitt
514-398-1663
andrea.miller-nesbitt@mcgill.ca

http://oregonexpat.wordpress.com/2013/10/2...
Bioinformatics resources: a primer
Bioinformatics resources: a primer
Bioinformatics resources: a primer
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Bioinformatics resources: a primer

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Overview of NCBI bioinformatics resources

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Bioinformatics resources: a primer

  1. 1. BIOINFORMATICS RESOURCES a primer A N DR EA MI L L E R -NESBI T T L I A I SON L I BR A R IA N AN DR EA .MI LL ER -NESBI T T@ MCGI LL.CA
  2. 2. Objectives By the end of this workshop you will be able to… • • • • • Understand differences between various bioinformatics resources available Do a basic search in NCBI Navigate between different NCBI resources Save your searches and set up alerts Know where to go for additional help
  3. 3. Bioinformatics is… “…us[ing] computers to store, retrieve, analyze or predict the composition or the structure of biomolecules” -Bioinformatics.org “…the integration of computers, databases and software into research projects that address large biological questions, or problems” -UBC, What is Bioinformatics? http://web.archive.org/web/20041210092942/http://bioinformatics.org/faq/ http://www.bioteach.ubc.ca/what-is-bioinformatics/
  4. 4. http://www.ncbi.nlm.nih.gov/genbank/genbankstats-2008/
  5. 5. Applications of bioinformatics http://deliverymatez.com/store/index.php?route=product/category&path=70, http://ftdtheotherdementia.com/hope-research.html http://www.bio.org/articles/agriculture-biotechnology-international-trade-fact-sheet, http://medicine.missouri.edu/obgyn/residency-research.html, http://www.csmi.org.cy/
  6. 6. Bioinformatics subject guide http://www.mcgill.ca/library/find/subjects/health/bioinformatics
  7. 7. Freely available resources
  8. 8. http://www.ncbi.nlm.nih.gov/Database/datamodel/
  9. 9. Types of resources Database vs Tool Databases •repositories of primary biological data • Ex. GenBank Tools •manipulate or analyze the data • Ex. BLAST, BindN http://www.appointmentsetter.net.au/telemarketing-vs-appointment-setting/
  10. 10. Types of resources Uncurated vs Curated Databases Uncurated •Raw datasets with no annotation • Ex. Nucleotide, Protein Curated •Include annotations describing the raw data • Ex. RefSeq, BioSystems http://www.appointmentsetter.net.au/telemarketing-vs-appointment-setting/
  11. 11. Let’s take a closer look… Uncurated (GenBank) Curated (RefSeq) Author submits NCBI creates record from existing data Only author can revise NCBI revises as new data emerge Multiple records for same loci are common Single records for each molecule of major organisms Records can contradict each other Data exchanged among INSDC members Exclusive NCBI database Akin to primary literature Akin to review article http://www.biotnet.org/sites/biotnet.org/files/documents/34/mod1-intro_h1_2011_seqdbs.pdf
  12. 12. Results display 1. Context—information about the sequence 2. Features—annotation of the sequence • 3. Complete list of features: http://www.insdc.org/documents/feature_table.html#7.3 http://www.ncbi.nlm.nih.gov/Sequin/sequin.hlp.html#Features Sequence—the sequence itself
  13. 13. Activity! http://www.camelcitydispatch.com/wp-content/uploads/2012/12/mad-scientist-movie1.jpg
  14. 14. Getting help
  15. 15. Questions? Andrea Miller-Nesbitt 514-398-1663 andrea.miller-nesbitt@mcgill.ca http://oregonexpat.wordpress.com/2013/10/23/ommatoiulus-moreletii-at-home-and-abroad/
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