PPT-Genome alignment Usman Roshan

Applications Genome sequencing on the rise Whole genome comparison provides a deeper understanding of biology Evolutionary history Noncoding regions Variant detection Methods General twofold approach. Genome Alignment in the Human Genome. Jian. Ma. Jian Ma | Sequence Comparison and Genome Alignment | 2015. 1. PowerPoint by Casey . Hanson. Introduction. This goals of the lab are as follows:. Gain experience using BLAST and Genome Browsers by looking at repeat families in the VHL gene.. transform. Heng. Li and Richard Durbin∗. Members of this presentation:. Yunji. Wang. Sree. . Devineni. Zhen Gao. Motivation. The first generation of hash table-based methods (e.g. MAQ) are:. Slow. Read Sequencing . Analysis. Jim Noonan. GENE 760. Sequence read lengths remain limiting. For most applications reads are . aligned. to a reference genome. Short reads contain inherently . limited information. 2. Some genomics history. 1995: first bacterial genome, . Haemophilus influenza. , 1.8 Mbp, sequenced at TIGR. first use of whole-genome shotgun for a bacterium. Fleischmann et al. 1995 became most-cited paper of the year (>3000 citations). Comparative Genomics. Eric Franzosa, PhD. 2 April 2014. From the notes of . CHARLES DARWIN. Mid-July 1837. What evolution is. Biological systems replicate. Replication introduces variation. Some variants replicate more. Jim Noonan. GENE 760. Sequence read lengths remain limiting. For most applications reads are . aligned. to a reference genome. Short reads contain inherently limited information. De novo . assembly of short reads is difficult. BIOS 234. June 1. Variant Detection Pipeline. Alignment. Variant Discovery and Genotyping. Prioritization and Filtering. Variant Interpretation. DNA Sequencing. Functional Validation / Clinical Assessment. Tandy Warnow. Departments of Computer Science and Bioengineering. Carl R. . Woese. Institute for Genomic Biology. The University of Illinois at Urbana-Champaign. http://tandy.cs.illinois.edu. O. r. a. Derek M Bickhart . Animal Genomics and Improvement Laboratory . Research Geneticist (Animal) . derek.bickhart@ars.usda.gov . Phone: (301) 504-8679 Fax: (301) 504-8092. USDA disclaimer. Disclaimers: Mention of trade names, commercial products, or companies in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture over others not mentioned. . (. dsenol@andrew.cmu.edu. ). Gurpreet S. Kalsi. 2. , . Zulal. Bingol. 3. , Can Firtina. 4. , Lavanya Subramanian. 5. ,. Jeremie Kim. 1,4. , Rachata Ausavarungnirun. 6,1. , Mohammed Alser. 4. , . Juan Gomez-Luna. BLAST. Local pairwise alignment heuristic. Faster than standard pairwise alignment programs such as SSEARCH, but less sensitive.. Online server: . http://www.ncbi.nlm.nih.gov/blast. BLAST. Given a query . DNA - the basics. Drew Berry – DNA animations. http://. www.youtube.com. /. watch?v. =. WFCvkkDSfIU&index. =4&list=PL9CBBEA5A85DBCDEF. Organisation of DNA. DNA is packed in Chromosomes . Karyotype: chromosome set of a species . Basic probability . and stats. Random variable. Probability of an event. Coin toss example. Independent random variables. Mean and variance of a random variable. Correlation between random variables. . https://damlasenolcali.github.io/. . Konstantinos Kanellopoulos, Joel . Lindegger. , Zulal . Bingol. , Gurpreet S. Kalsi, Ziyi Zuo, Can Firtina, Meryem Banu . Cavlak. , Jeremie S. Kim, Nika Mansouri Ghiasi, .