Throughput 400-600 million high-quality, filter-passed bases per run* 1 billion bases per day Run Time10 hours Read Length Modal length = 500 bases, Average length = 400 bases DataTrace data accepted by NCBI since 2005 http://www.454.com/products-solutions/system-features.asp
Summary of Capabilities ~ 10k per full run 454½ to 1 Million reads of 400bp ea = 200 to 400 Mb, 10hrs http://www.454.com/products-solutions/system-features.asp SOLiD½ Billion reads of 50 to 100bp ea= 25 to 50 Gb for 3 to 10 days http://www3.appliedbiosystems.com/AB_Home/applicationstechnologies/SOLiDSystemSequencing/overviewofsolidsystem/index.htm
Soft Genetics: http://www.softgenetics.com/NextGENe.html Soft Genetics: http://www.softgenetics.com/NextGENe.html “The NextGENe Condensation Tool™, solves the 3 critical problems” Reads too short High Error Rates Overwhelming Data Volume
For many applications, the data can be analyzed in four major steps: 1. Convert sample file format. 2. Condense sequence reads (polish data) Low frequency instrument errors Elongating the read lengths Optional reduction of number of reads to increase analysis speed 3. Align or assemble reads. 4. View and export results.
Apollo gene annotation of a genome region in Sebastes influenced by natural selection
UCSC Genome Browser http://genome.ucsc.eduhttp://genome.ucsc.edu) From Genes to Genomes in Non-Model Species
Learning Objectives Understand capabilities of emerging tools used in genetic analysis Verbal fluency in basic principles and practices of genetics Understand how geneticists study evolution at a variety of time scales Independent mastery and creative thought in one area of genetics via writing research proposal Assessment Demonstrate understanding of material through two midterms (30%) Presentations, case studies (25%) Write a research proposal (45%) http://www.juniata.edu/faculty/buonaccorsi/
http://www.pacificbiosciences.com/ http://www.pacificbiosciences.com/ 80,000 reads * 20,000 bp per read = 1.6GB for $100 in 10hrs start-finish
Cofactor Genomics http://www.cofactorgenomics.com/home/about/cofactor-gives-back/ http://www.cofactorgenomics.com/home/about/cofactor-gives-back/ NSF REU: student internships http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=5517&from=fund http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=5517&from=fund NSF CCLI 200k-250k http://www.nsf.gov/pubs/2009/nsf09529/nsf09529.html http://www.nsf.gov/pubs/2009/nsf09529/nsf09529.html Projects that: Build on the current understanding of how people learn Have the potential to transform undergraduate STEM education Research Coordination Networks in Biological Sciences (RCN) http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=11691&org=BIO http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=11691&org=BIO Other: Innovative approach to a well-defined, important problem
A guide to web resources http://bib.oxfordjournals.org/cgi/reprint/8/1/6
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