Bioinformatics resources: a primer
This document provides an introduction and overview of bioinformatics resources. It begins by outlining the objectives of understanding different bioinformatics databases and tools, learning how to search and navigate the National Center for Biotechnology Information (NCBI) database, and finding additional help. Definitions of bioinformatics are provided. The document then describes various applications of bioinformatics and directs the reader to a subject guide on bioinformatics resources. It proceeds to categorize major types of freely available bioinformatics resources as databases versus tools, and as curated versus uncurated databases. Specific examples like GenBank, BLAST, and RefSeq are outlined. The document concludes by providing contact information for questions.
![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/](https://image.slidesharecdn.com/bioinformaticsresourcesprimer-140223185142-phpapp01/85/Bioinformatics-resources-a-primer-3-320.jpg)
Bioinformatics resources: a primer
- 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… • • • • • 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/
- 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/
- 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 • 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
- 17. Getting help