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Welcome to Introduction to Bioinformatics Monday, 23 February 2009 Genome analysis / Viral Metagenomes. Genome analysis (Search for FMRP). (Flavors of Blast). Example with unknown sequence. Exam 1 retrospective (Problem 9 – coverage). Edwards & Rohwer – Viral Metagenomes.
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Welcome toIntroduction to BioinformaticsMonday, 23 February 2009Genome analysis / Viral Metagenomes • Genome analysis (Search for FMRP) (Flavors of Blast) • Example with unknown sequence • Exam 1 retrospective (Problem 9 – coverage) • Edwards & Rohwer – Viral Metagenomes • Mapping and Loops This demonstration is best viewed as a slide show,enabling you to simulate a session and make changes in cursor position more obvious.To do this, click Slide Show on the top tool bar, then View show.
Query Database Search for FMRP
Query Database Search for FMRP
Search for FMRP Query Database
Search for any sequence Tobacco Mg chelatase (chlorophyll biosynthesis)100% identity, E-value = 0
Search for any sequence Tobacco Mg chelatase (chlorophyll biosynthesis)40% identity, E-value = 3 x 10-4
Search for any sequence Tobacco Mg chelatase (chlorophyll biosynthesis)100% identity, E-value = 0
Search for any sequence Tobacco Mg chelatase (chlorophyll biosynthesis)100% identity, E-value = 0 Human melanocortin receptor Upstream region99% identity, E-value = 0 Meaning?
Welcome toIntroduction to BioinformaticsMonday, 23 February 2009Genome analysis / Viral Metagenomes • Genome analysis (Search for FMRP) (Flavors of Blast) • Example with unknown sequence • Exam 1 retrospective (Problem 9 – coverage) • Edwards & Rohwer – Viral Metagenomes • Mapping and Loops
Exam 1 retrospective SQ14.From figures given in the text and in Table 1, check the accuracy of each of the following…
SQ14.From figures given in the text and in Table 1, check the accuracy of each of the following… Exam 1 retrospective
Edwards & Rohwer (2005)What is metagenomics? SQ2. Genome sequencing vs metagenomic sequencing? What special challenges?
FOR-EACH variable name Control section – Determines form of iteration Initialization section – Initializes loop variables before the loop begins Variable update section – Resets loop variables each iteration Body – Forms to be iterated Results section – Determines the result returned by the loop Final action – To be performed after last iteration Loops Workspace Undo | Redo Results