PPT-Algorithms for Mitochondrial Genome Assembly and Haplogroup Assignment from Low-Coverage

Fahad Alqahtani Supervisor Dr Ion Măndoiu Associate Advisors Dr Mukul Bansal amp Dr Derek Aguiar Computer Science amp Engineering Department University of Connecticut Outline Background. sequencing . for . identification,. detection, . and control of . Bactrocera dorsalis (. Hendel. ). and other Tephritid pests. Thomas Walk, Scott . Geib. USDA-ARS Pacific Basin Agricultural Research Center, Hilo HI. 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 . 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 . genome . assembly. Sorin. . Istrail. CSCI1820 Short-read genome assembly algorithms. 3/6/2014. 1. Genomathica Assembler. Mathematica. notebook for genome assembly simulation. Assembler can be found at: . Multi-Channel Wireless Networks. Donghoon Shin, . Saurabh. . Bagchi. and . Chih. -Chun Wang. Dependable Computing Systems Lab (DCSL). School of Electrical and Computer Engineering. Purdue University. Purbendra yogi. Introduction. Genome assembly is the process of taking of many short DNA sequences and combine them to form original chromosome.. First generation Assembly began in the late 1980’s and early 1990’s..  . Nancy Phang. June 4, 2004. Contig266405. is 23.3 kb. FGENESH. BLASTn. BLASTp. tBLASTn. Description. Gene 1. 6e-17. 2.9. . 3e-38. . P063968 Lotus . japonicus. mature nodule Lotus . japonicus. Chris Fields. Genome Assembly | Saba Ghaffari | 2020. 1. PowerPoint by Saba Ghaffari. Introduction. Exercise . Perform a bacterial genome assembly using PacBio HiFi data.. Evaluation and comparison of different datasets and parameters.. 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.. Mitochondrial DNA Mitochondrial DNA (mtDNA) is DNA contained in the mitochondria in our cells - these are the energy - generating structures commonly referred to as the 'batteries' or 'powerhouses' 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.