Overview of NCBI bioinformatics resources

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. Objectives
By the end of this workshop you will be able to…
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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. 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. http://www.ncbi.nlm.nih.gov/genbank/genbankstats-2008/

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. Bioinformatics subject guide
http://www.mcgill.ca/library/find/subjects/health/bioinformatics

7. Freely available resources

8. http://www.ncbi.nlm.nih.gov/Database/datamodel/

10. 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/

11. 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/

12. 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

13. Results display
1.
Context—information about the sequence
2.
Features—annotation of the sequence
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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

14. Activity!
http://www.camelcitydispatch.com/wp-content/uploads/2012/12/mad-scientist-movie1.jpg

17. Getting help

18. 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/