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. Denovo genome Denovo genome outline outline novogenome from contigs from assembled contigs annotation Denovo genome Denovo genome Reads contig Gene Gene Annotation Gene Annotation Forgene David Griffith, Voltaire Velazco. University of Wollongong. with very significant inputs from. John Robinson (Lauder). Frank Hase (KIT). Graham Kettlewell (UoW). IFS125 FT spectrometer. IFS125 interferometer. Image from http://graphics.cs.cmu.edu/courses/15-463/2010_fall/. A look into the past. http://blog.flickr.net/en/2010/01/27/a-look-into-the-past/. A look into the past. Leningrad during the blockade. 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. Scott Walmsley, PhD. Research Instructor, Department Pharmaceutical Sciences. Skaggs School of Pharmacy. Outline . What is and why perform Multiple . S. equence . A. lignment (MSA)?. Pre-requisite knowledge. 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. Xuhua Xia. xxia@uottawa.ca. http://dambe.bio.uottawa.ca. Xuhua Xia. Slide . 2. Normal and Thalassemia HBb. Are the two genes homologous?. What evolutionary change can you infer from the alignment? . What is the consequence of the evolutionary change?. BIOS 234. June 1. Variant Detection Pipeline. Alignment. Variant Discovery and Genotyping. Prioritization and Filtering. Variant Interpretation. DNA Sequencing. Functional Validation / Clinical Assessment. BMI 877. Colin Dewey. colin.dewey@wisc.edu. March 14, 2017. Overview. What does it . mean . to . align. sequences?. How do we cast sequence alignment as a . computational problem?. What . algorithms . 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. . . Usman. . Effendi . adalah. . salah. . satu. . sastrawan. Indonesia yang . lahir. . di. Padang . pada. 13 Mei 1903 . dan. . wafat. . di. Jakarta 24 Mei . 1979.. Riwayat. . Pendidikan. :. 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 . G-OnRamp Beta Users Workshop. Wilson Leung. 07/2016. Outline. Obtain genome assemblies from NCBI. Transfer . large genomics datasets to Galaxy. Common bioinformatics file formats . D. atatypes in Galaxy.