This Bioinformatics Workshop is a three-day intensive training workshop that AMBL offers to a professional audience. Current topics in bioinformatics, genomics and proteomics are covered. Participants are introduced to common tools and database resources for bioinformatics. Practical exercises and guided tours give workshop participants hands-on experience with bioinformatics searches, tasks, and analyses.
This workshop was hosted at the Michael Smith Labs in February 2008.
Day 1 – Links, References & Supplementary Readings
Lecture Materials
What is Bioinformatics?
Fox J. http://www.scq.ubc.ca/what-is-bioinformatics/
Sequencing Technologies
Genome Projects: Uncovering the Blueprints of Biology
Kae H. http://www.scq.ubc.ca/genome-projects-uncovering-the-blueprints-of-biology/
DNA Sequencing with Solexa Technology:
http://www.illumina.com/downloads/SS_DNAsequencing.pdf
Molecular biology. Site-seeing by sequencing.
Fields S. Science 316 (2007) 1441-2. [PMID: 17556576]
Whole-genome re-sequencing.
Bentley DR. Curr Opin Genet Dev. 16 (2006) 545-52. [PMID: 17055251]
Public Sequence Databaseshttp://www.ncbi.nlm.nih.gov/
Database resources of the National Center for Biotechnology Information.
Wheeler DL et al. Nucleic Acids Res. 36 (2008) D13-21. [PMID: 18045790]
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 Tutorial from NLM
http://www.nlm.nih.gov/bsd/pubmed_tutorial/m1001.html
Practical Exercises:
Retrieve records annotated with a given biological feature (e.g., promoter)
DAY 2 – Links, References & Supplementary Readings
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 25 (1997) 3389-3402. [PMID: 9254694]
Practical Exercises:
>DinoDNA from JURASSIC PARK p. 103 nt 1-1200
GCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGC
GGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCG
TGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGC
TGCTCACGCTGTACCTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTG
CCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAA
AGTAGGACAGGTGCCGGCAGCGCTCTGGGTCATTTTCGGCGAGGACCGCTTTCGCTGGAG
ATCGGCCTGTCGCTTGCGGTATTCGGAATCTTGCACGCCCTCGCTCAAGCCTTCGTCACT
CCAAACGTTTCGGCGAGAAGCAGGCCATTATCGCCGGCATGGCGGCCGACGCGCTGGGCT
GGCGTTCGCGACGCGAGGCTGGATGGCCTTCCCCATTATGATTCTTCTCGCTTCCGGCGG
CCCGCGTTGCAGGCCATGCTGTCCAGGCAGGTAGATGACGACCATCAGGGACAGCTTCAA
CGGCTCTTACCAGCCTAACTTCGATCACTGGACCGCTGATCGTCACGGCGATTTATGCCG
CACATGGACGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAA
CAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAA
GCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGG
CTTTCTCAATGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTG
ACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCA
ACACGACTTAACGGGTTGGCATGGATTGTAGGCGCCGCCCTATACCTTGTCTGCCTCCCC
GCGGTGCATGGAGCCGGGCCACCTCGACCTGAATGGAAGCCGGCGGCACCTCGCTAACGG
CCAAGAATTGGAGCCAATCAATTCTTGCGGAGAACTGTGAATGCGCAAACCAACCCTTGG
CCATCGCGTCCGCCATCTCCAGCAGCCGCACGCGGCGCATCTCGGGCAGCGTTGGGTCCT
>DinoDNA from THE LOST WORLD p. 135
GAATTCCGGAAGCGAGCAAGAGATAAGTCCTGGCATCAGATACAGTTGGAGATAAGGACG
GACGTGTGGCAGCTCCCGCAGAGGATTCACTGGAAGTGCATTACCTATCCCATGGGAGCC
ATGGAGTTCGTGGCGCTGGGGGGGCCGGATGCGGGCTCCCCCACTCCGTTCCCTGATGAA
GCCGGAGCCTTCCTGGGGCTGGGGGGGGGCGAGAGGACGGAGGCGGGGGGGCTGCTGGCC
TCCTACCCCCCCTCAGGCCGCGTGTCCCTGGTGCCGTGGGCAGACACGGGTACTTTGGGG
ACCCCCCAGTGGGTGCCGCCCGCCACCCAAATGGAGCCCCCCCACTACCTGGAGCTGCTG
CAACCCCCCCGGGGCAGCCCCCCCCATCCCTCCTCCGGGCCCCTACTGCCACTCAGCAGC
GGGCCCCCACCCTGCGAGGCCCGTGAGTGCGTCATGGCCAGGAAGAACTGCGGAGCGACG
GCAACGCCGCTGTGGCGCCGGGACGGCACCGGGCATTACCTGTGCAACTGGGCCTCAGCC
TGCGGGCTCTACCACCGCCTCAACGGCCAGAACCGCCCGCTCATCCGCCCCAAAAAGCGC
CTGCTGGTGAGTAAGCGCGCAGGCACAGTGTGCAGCCACGAGCGTGAAAACTGCCAGACA
TCCACCACCACTCTGTGGCGTCGCAGCCCCATGGGGGACCCCGTCTGCAACAACATTCAC
GCCTGCGGCCTCTACTACAAACTGCACCAAGTGAACCGCCCCCTCACGATGCGCAAAGAC
GGAATCCAAACCCGAAACCGCAAAGTTTCCTCCAAGGGTAAAAAGCGGCGCCCCCCGGGG
GGGGGAAACCCCTCCGCCACCGCGGGAGGGGGCGCTCCTATGGGGGGAGGGGGGGACCCC
TCTATGCCCCCCCCGCCGCCCCCCCCGGCCGCCGCCCCCCCTCAAAGCGACGCTCTGTAC
GCTCTCGGCCCCGTGGTCCTTTCGGGCCATTTTCTGCCCTTTGGAAACTCCGGAGGGTTT
TTTGGGGGGGGGGCGGGGGGTTACACGGCCCCCCCGGGGCTGAGCCCGCAGATTTAAATA
ATAACTCTGACGTGGGCAAGTGGGCCTTGCTGAGAAGACAGTGTAACATAATAATTTGCA
CCTCGGCAATTGCAGAGGGTCGATCTCCACTTTGGACACAACAGGGCTACTCGGTAGGAC
CAGATAAGCACTTTGCTCCCTGGACTGAAAAAGAAAGGATTTATCTGTTTGCTTCTTGCT
GACAAATCCCTGTGAAAGGTAAAAGTCGGACACAGCAATCGATTATTTCTCGCCTGTGTG
AAATTACTGTGAATATTGTAAATATATATATATATATATATATATCTGTATAGAACAGCC
TCGGAGGCGGCATGGACCCAGCGTAGATCATGCTGGATTTGTACTGCCGGAATTC
Accessing Genome Annotations with Genome Browsers
UCSC Genome Browser
http://genome.cse.ucsc.edu/
Ensembl Genome Browser
http://www.ensembl.org/index.html
NCBI MapViewer
http://www.ncbi.nlm.nih.gov/mapview/index.html
DAY 3 – Links, References & Supplementary Readings
Lecture Materials
Discovering GEO – the Gene Expression Omnibus
The use and analysis of microarray data.
Butte A. Nat Rev Drug Discov. 12 (2002) 951-60. [PMID: 12461517]
NCBI GEO: mining tens of millions of expression profiles–database and tools update.
Barrett T, et al. Nucleic Acids Res. 35 (2007) D760-5. [PMID: 17099226]
GEO: the Gene Expression Omnibus
http://www.ncbi.nlm.nih.gov/projects/geo/info/GEOHandoutFinal.pdf
Pathway Resources for Systems Biology
Pathway information for systems biology.
Cary MP, Bader GD, Sander C. FEBS Letters 579 (2005) 1815-1820 [PMID: 15763557]
Cytoscape
http://cytoscape.org/index.php
Finding online tools & resources for Life Sciences research
Bioinformatics Links Directory
http://bioinformatics.ca/links_directory/
Conducting research on the web: 2007 update for the bioinformatics links directory.
Fox JA, McMillan S, Ouellette BF. Nucleic Acids Res. 35 (2007) W3-5. [PMID: 17586821]
NAR Database Collection
http://www.oxfordjournals.org/nar/database/c