PPT-On Genome Assembly

Abhiram Ranade IIT Bombay Genome Constituent of living cells that determines hereditary characteristics aka DNA Sequence of nucleobases A denine G uanine T hymine C ytosine. 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 Mayo/UIUC Summer . C. ourse in Computational Biology. Session Outline. Genome sequencing. Schematic overview of genome assembly. (a) DNA is collected from the biological sample and sequenced. (b) The output from the sequencer consists of many billions of short, unordered DNA fragments from random positions in the genome. (c) The short fragments are compared with each other to discover how they overlap. (d) The overlap relationships are captured in a large assembly graph shown as nodes representing . By Kevin Chen, . Lior. . Pachter. PLoS. Computational Biology, 2005. David Kelley. State of . metagenomics. In July 2005, 9 projects had been completed.. General challenges were becoming apparent. Paper focuses on computational problems. C. onifer . G. enome, Loblolly Pine. Jill Wegrzyn. Pieter . de Jong, . Chuck Langley, Dorrie Main, Keithanne Mockaitis, . Steven Salzberg, . Kristian. . Stevens. , Nick . Wheeler, Jim . Yorke, . Aleksey . Mayo/UIUC Summer . C. ourse in Computational Biology. Session Outline. Genome sequencing. Schematic overview of genome assembly. (a) DNA is collected from the biological sample and sequenced. (b) The output from the sequencer consists of many billions of short, unordered DNA fragments from random positions in the genome. (c) The short fragments are compared with each other to discover how they overlap. (d) The overlap relationships are captured in a large assembly graph shown as nodes representing . Kerstin Lindblad-Toh1 et al.. Presentation by:. Keara Flores. Gustavo Diaz Cruz. Background. Human genome sequenced in 2003 and researchers learned 1.5% of it codes proteins. . 2005 Lindblad-Toh and colleagues begin effort to sequence domestic dog producing a SNP map allows for comparative analysis of the mammalian genome. . terrestris. , . the buff-tailed bumble bee. Native to Europe. A managed pollinator. Commercially available. Reared in greenhouses. Important pollinator in greenhouses and in agricultural fields. Adorable. Please go to husky CT and complete student evaluations !. PSI . (. position-specific iterated) . BLAST. The NCBI page described PSI blast as follows: . “. Position-Specific Iterated BLAST (PSI-BLAST) provides an automated, easy-to-use version of a "profile" search, which is a sensitive way to look for sequence homologues. . Genome: the total number of genes in an individual.. Human Genome- approx. 20,000 genes on the 46 human chromosomes.. Human Genome Project (HGP). Ongoing effort to completely map and sequence our genome.. School of Engineering. Assembler. Reference. Abyss 1.5.1. Simpson et al., J. T., Wong, K., Jackman, S. D., Schein, J. E., Jones,. . S. J., and . Birol. , I. (2009). Abyss: a parallel assembler for. . 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. . Tutorial. Pei-Chen Peng. Linux+Genome Assembly | Shounak Bhogale | 2019. 1. Step 1A: Save login credential. Linux+Genome Assembly | Shounak Bhogale | 2019. 2. For viewing and manipulating the files needed for this laboratory exercise, insert your flash drive.. assembly. Illumina. Subsample. Summarize. Assemble. Polish. Evaluate. Evaluate . unpolished. Hybrid assembly. Pacbio. . Subsample. Summarize. Assemble. Polish. Evaluate. Evaluate . polished. Parameter exploration. Fahad Alqahtani and Ion Mandoiu. University of Connecticut. Computer Science and Engineering Department. Outline. Introduction & prior . w. ork. Our approach. Preliminary results. Conclusion and future work.