PPT-Motif discovery GENOME 559: Introduction to Statistical and Computational Genomics

Prof William Stafford Noble Stuff folks liked Good pace x3 Powerpoint was easy to follow x2 Really appreciate reading the program step by step x2 Helpful to go over the sample problems at the beginning of class. analyze . your data with a mouse click. Igor Makunin. i.makunin@uq.edu.au. QAAFI, UQ, April 8, 2015. Research. Computing. Centre. @ UQ. Genomics Virtual Laboratory. Genome scale experiments are relatively cheap and very popular. NHGRI strategic plan. What does the NIH think genomics should be for the next 10 years?. [Nature, Feb. 2011]. The Essence of Genomics. (according to NHGRI). Comprehensiveness. . Genomics . aims to generate complete data sets. Although relatively easy to define and measure for a genome sequence, attaining comprehensiveness can be more challenging for other targets (for example, functional genomic elements or the ‘proteome’). NHGRI strategic plan. What does the NIH think genomics should be for the next 10 years?. [Nature, Feb. 2011]. The Essence of Genomics. (according to NHGRI). Comprehensiveness. . Genomics . aims to generate complete data sets. Although relatively easy to define and measure for a genome sequence, attaining comprehensiveness can be more challenging for other targets (for example, functional genomic elements or the ‘proteome’). selection, . regulation, epigenomics, . disease. Manolis Kellis. MIT Computer Science & Artificial Intelligence Laboratory. Broad Institute of MIT and Harvard. Recombination breakpoints. Family Inheritance. Prof. William Stafford Noble. A dictionary organizes linked information.. Examples:. - word and definition. - name and phone number. - name and DNA sequence. - username and password. If you know the first entry, you can quickly and easily get the second one..  . I. Genetic, Cytological, and Physical Maps. II. Human Genome Project. A. . Goals of the Human Genome Project. B. . Public and Private First Drafts of the Human Genome Sequence. Prof. William Stafford Noble. Opening files. The open() command returns a file object.. <. filehandle. > = open(<filename>, <access type>). Python can read, write or append to a file:. Prof. William Stafford Noble. for. . loop review. block of code. for <element> in <object>:. <statement>. <statement>. . . .. <last statement>. . <element>. is a newly created variable name. You . selection, . regulation, epigenomics, . disease. Manolis Kellis. MIT Computer Science & Artificial Intelligence Laboratory. Broad Institute of MIT and Harvard. Goal: A systems-level understanding of genomes and gene regulation:. “. User facility. providing high-throughput DNA sequencing & analysis in support of DOE missions in alternative . energy. , . carbon cycling . & . bioremediation. .”. Opened in 1999. ~240 UC Employees. Genomics and Society Nature (2014) “ …disorders not readily explained by standard tests can sometimes be diagnosed through genome sequencing and analysis.” The Origin of “Genomics& from NHGRI’s . Planning . Workshop on the Future Opportunities . for . Genome Sequencing . & Beyond. Mark Gerstein & Rick Myers. Recommendations related to genome function. . Part 1: Workshop summary (Mark). Bionano Genomics, San Diego, California, United States of America. Abstract. Pat Lynch, PhD. Background. Generating high-quality finished genomes replete with accurate identification of structural variation and high completion (minimal gaps) remains challenging using short read sequencing technologies alone. The . CSE291: Personal Genomics for . Bioinformaticians. 01/. 10/17. The personal genomics revolution. 23andMe. : >1 million customers . (. $200). Genographic. Project: . >800,000 customers ($150). Family Tree DNA: .