BIOINFORMATICS RESOURCES a primerANDREA MILLER-NESBITT

LIAISON L IBRARIAN

ANDREA.MILLER-NESBITT@MCGILL.CA

ObjectivesBy 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

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/

http://www.ncbi.nlm.nih.gov/genbank/genbankstats-2008/

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/

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 resourcesDatabase vs ToolDatabases

•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/

Types of resources

http://www.appointmentsetter.net.au/telemarketing-vs-appointment-setting/

Uncurated vs Curated DatabasesUncurated

•Raw datasets with no annotation• Ex. Nucleotide, Protein

Curated

•Include annotations describing the raw data• Ex. RefSeq, BioSystems

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

Results display1. Context—information about the sequence

2. Features—annotation of the sequence• Complete list of features:

http://www.insdc.org/documents/feature_table.html#7.3http://www.ncbi.nlm.nih.gov/Sequin/sequin.hlp.html#Features

3. Sequence—the sequence itself

Activity!

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

Getting help

Questions?

http://oregonexpat.wordpress.com/2013/10/23/ommatoiulus-moreletii-at-home-and-abroad/

Andrea Miller-Nesbitt514-398-1663

andrea.miller-nesbitt@mcgill.ca