Laboratory Bioinformatics 2010

Posted by | May 11, 2010 | RESOURCES, UNIVERSITY+ | No Comments

LABORATORY BIOINFORMATICS WORKSHOP 2010

This workshop focuses on bioinformatics techniques for practical use in the laboratory. Hands-on exercises for retrieving data, primer design, BLAST searching, and genomics data navigation are covered. Primarily aimed at researchers who are new to the area, or familiar but require a quick updating, where content covered can be tailored to laboratory needs.

Looking for the BLAST practical exercises? Scroll down or Click here.

Workshop Evalution

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2009 Workshop Participants describe the workshop:

A fairly intensive course that managed to achieve a good mix between overview information and in depth details. Therefore, it highly recommendable for scientists who are new to the field of bioinformatics and provides and ideal starting point to gain further practical knowledge using bioinformatic tools. It also provided information specific to participants individual requirements.

Incredible way of fast learning about the most popular bioinformatics tools available, as well as practical examples that open a big world of ideas of how to make research. I feel much more confident now that I can quickly hone in on pertinent information and understand what I retrieve. This workshop was extremely valuable in calling my attention to many of the resources available in the public domain and how to use features I was not previously aware of. It is worth the time for this workshop!

All of the course materials for this workshop are available online.

Jump to:
Day 1
Day 2
Day 3
Links

Day 1 – Links, References & Supplementary Readings

pdfLecture Materials

What is Bioinformatics?
Fox J. http://www.scq.ubc.ca/what-is-bioinformatics/

Public Database Resources

National Center for Biotechnology Information
http://www.ncbi.nlm.nih.gov/

Database resources of the National Center for Biotechnology Information.
Wheeler DL et al. Nucleic Acids Res. 38 (2010) D5-D16. [PMID: 19910364]

The “About Entrez” page at the NCBI
http://www.ncbi.nlm.nih.gov/Database/index.html

Model of Entrez Databases from NCBI
http://www.ncbi.nih.gov/Database/datamodel/index.html

PubMed Online Training from NLM
http://www.nlm.nih.gov/bsd/disted/pubmed.html

PubMed Redesign, NLM Technical Bulletin
http://www.nlm.nih.gov/pubs/techbull/so09/so09_pm_redesign.html

Practical Exercises:

  1. Entrez Database Searching Scenario
  2. You notice a gene of interest in the literature and you want to find out more…

    pdf Entrez Database Searching Scenario

  3. Retrieve records annotated with a given biological feature (e.g., promoter)
  4. This Sample GenBank Record gives a detailed description of each field in a GenBank record. For this exercise, you will try two search approaches. Approach A begins in the Entrez Nucleotide database while Approach B begins in the Entrez Gene database

    pdf Retrieve records annotated with a given biological feature (e.g., promoter)

    Adapted from: NCBI Advanced Workshop for Bioinformatics Information Specialists

  5. Exercises to try on your own
  6. pdfDay 1 – Take Home Exercises (optional)

DAY 2 – Links, References & Supplementary Readings

pdf Lecture Materials

Sequence Similarity Searching

BLAST: Basic Local Alignment Search Tool
http://www.ncbi.nlm.nih.gov/blast/Blast.cgi

Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ J. Mol. Biol. 215 (1990) 403-410. [PMID: 2231712]

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaeffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ Nucleic Acids Res. 25 (1997) 3389-3402. [PMID: 9254694]

NCBI BLAST: a better web interface. Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL Nucleic Acids Res. 36 (2008) W5-W9 [PMID: 18440982]

Designing and Testing Primers with NCBI’s Primer-BLAST:

NCBI Primer-BLAST service:
http://www.ncbi.nlm.nih.gov/tools/primer-blast/

General Concepts for PCR Primer Design.
Dieffenback CW, Lowe TMJ, Dveksler GS Genome Research 3 (1993) S30-37 [PMID:8118394]

Looking for help with the advanced parameters of Primer-BLAST?
Try the Primer3 help page.

Multiple Sequence Alignments – Comparing Sets of Protein Sequences

Bioinformatics Tools for Multiple Sequence Alignments hosted at the EBI
http://www.ebi.ac.uk/Tools/msa/

ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.
http://www.ebi.ac.uk/Tools/clustalw2/
Download the current version of ClustalX here: http://www.clustal.org/

MUSCLE stands for MUltiple Sequence Comparison by Log-Expectation.
http://www.ebi.ac.uk/Tools/muscle/
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput [PMID: 15034147]

COBALT: constraint-based alignment tool for multiple protein sequences
http://www.ncbi.nlm.nih.gov/tools/cobalt/
Papadopoulos JS and Agarwala R, Bioinformatics 23:1073-79, 2007 [PMID: 17332019]

Expasy Proteomics Server, a server dedicated to the analysis of protein sequences and structures.
http://ca.expasy.org/

Practical Exercises:

  1. Basic BLAST:
  2. An astonishing techique for recovering and cloning dinosaur DNA has been discovered. Now mankind’s most thrilling fantasies have come true. Creature extinct for eons roam Jurassic Park with their awesome prescence and proufound mystery, and all the world can visit them — for a price. Until something goes wrong …

    txtDinoDNA from JURASSIC PARK p. 103 nt 1-1200

    txtDinoDNA from THE LOST WORLD p. 135

  3. Searching with sets of sequences and/or with small custom databases:
  4. A salmonid EST genomic study: genes, duplications, phylogeny and microarrays.
    Koop BF, von Schalburg KR, Leong J, Walker N, Lieph R, Cooper GA, Robb A, Beetz-Sargent M, Holt RA, Moore R, Brahmbhatt S, Rosner J, Rexroad CE, McGowan CR, Davidson WS BMC Genomics 9 (2008) 545 [PMID: 19014685]

    txtFASTA file with Salmon ESTs from Koop et al.

    txtZebrafish hemoglobin alpha adult-1 (hbaa1)

  5. Primer BLAST:
  6. NCBI now offers Primer-BLAST, a Web service for designing target specific oligonucleotide primers for use in PCR protocols. This service integrates primer designing code from the popular Primer3 software with a specificity check that uses a custom BLAST search.
    source: NCBI News, November 2008

    pdf Use Primer-BLAST to design primers for UNG transcript variants

  7. Generate a Multiple Sequence Alignment with Globin proteins
  8. txtSave this file to your desktop.
    Download the current version of ClustalX here: http://www.clustal.org/

  9. Exercises to try on your own
  10. pdfDay 2 – Take Home Exercises (optional)

DAY 3 – Links, References & Supplementary Readings

pdf Lecture Materials

Accessing Genome Annotations with Genome Browsers
UCSC Genome Browser
http://genome.cse.ucsc.edu/

Ensembl Genome Browser
http://www.ensembl.org/index.html

NCBI Map Viewer
http://www.ncbi.nlm.nih.gov/projects/mapview/

Artemis
http://www.sanger.ac.uk/resources/software/artemis/
Artemis: sequence visualization and annotation. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA and Barrell B, Bioinformatics 2000;16;10;944-5 [PMID: 11120685]

Pathway Resources for Systems Biology
Pathguide: the pathway resource list
http://www.pathguide.org/

Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search.
http://www.pathwaycommons.org/pc/

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.
http://cytoscape.org/

Pathway information for systems biology.
Cary MP, Bader GD, Sander C. Febs Lett 8 (2005) 1815-20 [PMID: 15763557]

Laboratory Bioinformatics Links:


The essentials:
NCBI – http://www.ncbi.nlm.nih.gov/
BLAST – http://blast.ncbi.nlm.nih.gov/Blast.cgi
NCBI Primer-BLAST – http://www.ncbi.nlm.nih.gov/tools/primer-blast/
Primer3 http://frodo.wi.mit.edu/primer3/input.htm
ClustalW2 http://www.ebi.ac.uk/Tools/clustalw2/
MUSCLE http://www.ebi.ac.uk/Tools/muscle/
COBALT http://www.ncbi.nlm.nih.gov/tools/cobalt/
Expasy http://ca.expasy.org/
UCSC Genome Browser http://genome.cse.ucsc.edu/
Ensembl Genome Browser http://www.ensembl.org/index.html
NCBI Map Viewer http://www.ncbi.nlm.nih.gov/projects/mapview/
Artemis http://www.sanger.ac.uk/resources/software/artemis/
GEO http://www.ncbi.nlm.nih.gov/geo/index.cgi
Pathguide http://www.pathguide.org/
Pathway Commons http://www.pathwaycommons.org/pc/
Cytoscape http://cytoscape.org/

Useful utilities:
PlasMapper: a web server for drawing and auto-annotating plasmid maps. Dong X, Stothard P, Forsythe IJ, Wishart DS Nucleic Acids Res. 32 (2004) W660-664. [PMID:15215471]

Are you looking for a bioinformatics tool that’s not covered here?

Search the Bioinformatics Links Directory:
http://bioinformatics.ca/links_directory/index.php
Keeping pace with the data: 2008 update on the Bioinformatics Links Directory. Brazas MD, Fox JA, Brown T, McMillan S, Ouellette BFF Nucleic Acids Res. 36 (2008) W2-W4. [PMID: 18586831]

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