PPT-Repetitive DNA and next-generation sequencing: computationa

Chen Bichao TJ Treangen  SL Salzberg Nature Reviews Genetics 2011 5 Scope Introduction of Repetitive DNA 1 2 3 4 Mapping Assembly De novo Assembly RNA Seq Conclusions. Learning Objectives. Recap how DNA probes and DNA hybridisation is used to locate specific genes.. Learn how the exact order of nucleotides on a strand of DNA can be determined.. Learn how restriction mapping can be used to determine nucleotide sequences.. MOLECULAR BIOLOGY TECHNIQUES II.. Polymerase Chain Reacton – PCR. DNA sequencing. Amplification of specific DNA fragments. MOLECULAR BIOLOGY – PCR. Cloning and/ or isolation from a genomic library . Assembly, and Alignment Methods . Andy Nagar. Agenda. Background. Next Generation Sequencing. Sequence Assembly. Sequence Alignment. Traditional Alignment Algorithms. Next Generation Alignment Algorithms. Craig A. . Praul. Co- Director . Genomics Core Facility. Huck Institutes of the Life Sciences. Penn State University. A very short history of DNA sequencing. I started from the conviction that, if different DNA species exhibited . Lenka Veselovská. Laboratory of Developmental Biology and Genomics . Next Generation Sequencing (NGS) . M. odern high-throughput DNA sequencing technologies. parallel, rapid . Decreasing price, time, workflow complexity, error rate. A I . Bhat. Indian Institute of Spices Research. Calicut. DNA sequencing. Chain termination method . (. Sangers. . et a. l., 1977): In this method, the sequence of a single stranded DNA molecule is determined by enzymatic synthesis of complementary polynucleotide chains, these chains terminating at specific nucleotide positions.. Ion . Mandoiu. Computer Science and Engineering Department. University of Connecticut. Outline. Background on high-throughput sequencing. Identification of tumor-specific . epitopes. Estimation of gene and . Hardison. Genomics . 3_2. 1. 1/20/14. Second generation sequencing. Michael . Metzker. review. (2010) Nature Reviews Genetics . 11. : 31-46. 1/20/14. 2. Two generations of sequencing technology. Feature. How we obtain the sequence of nucleotides of a species. …ACGTGACTGAGGACCGTG. CGACTGAGACTGACTGGGT. CTAGCTAGACTACGTTTTA. TATATATATACGTCGTCGT. ACTGATGACTAGATTACAG. ACTGATTTAGATACCTGAC. TGATTTTAAAAAAATATT…. David . Tse. . Dept. of EECS. U.C. Berkeley. LIDS Student Conference. MIT. Feb. 2, 2012. Research supported by NSF Center for Science of Information.. TexPoint fonts used in EMF: . A. A. A. A. A. A. Dr. . Sudha. . Kumari. Assistant Professor. Department of Veterinary Microbiology. Bihar Animal Sciences University, Patna. INTRODUCTION . The . First, anneal the primer to the DNA template (must be single stranded):Then split the sample into four aliquots including the following nucleotides: When a DNA polymerase (e.g. Klenow fragment) ispro The Sanger method. DNA sequencing is the primary method for gene and protein characterization. . (protein sequence can be predicted from DNA sequence). . https://. www.illumina.com. /techniques/sequencing/. the DNA sequencing?. DNA sequencing determines the order of the four chemical building blocks - called "bases" - that make up the DNA molecule. . The . sequence tells scientists the kind of genetic information that is carried in a particular DNA segment.