PPT-De Novo Assembly of Mitochondrial Genomes from Low Coverage Whole-Genome Sequencing Reads

Fahad Alqahtani and Ion Mandoiu University of Connecticut Computer Science and Engineering Department Outline Introduction amp prior w ork Our approach Preliminary results Conclusion and future work. 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 . From Swab to Publication. Madison I. Dunitz. 1. , David A. Coil. 1. , Jenna M. Lang. 1. , Guillaume Jospin. 1. , Aaron E. Darling. 2. , Jonathan A. Eisen. 1. UC Davis Genome Center. 1. University of California, Davis; . 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. 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 . DNA. Double helix. Bases. Sequence. Gene . Key words. Genome . Genome sequencing. Species . Human Genome Project. DNA. is found in the nucleus of a cell. It is a long molecule that carries a set of codes to make you unique.. shinisaurus. . crocodilurus. Jian . gao. , . qiye. li, . zongji. . wang. , yang . zhou. , . paolo. . martelli. , fang li, . zijun. . xiong. , . jian. . wang. , . huanming. yang, and . guojie. . Dr. Vladimir Teif. BS222 – Genome Science Lecture 1. Welcome to BS222 Genome Science!. Meet your lecturers. Vladimir Teif. (module supervisor). Leonard . Schalkwyk. Patrick . Varga-Weisz. Jordi . Paps. 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.. Fahad Alqahtani. Supervisor: Dr. Ion Măndoiu. Associate Advisors: Dr. Mukul Bansal & Dr. Derek Aguiar. Computer Science & Engineering Department. University of Connecticut. Outline. Background. 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. Modified from Dan Russell. (Relevant) Trivia. How many base pairs (bp) are there in a human genome?. How many protein coding genes are in the Human genome. How much did it cost to sequence the first human genome?. Update and rationale. Low-pass sequencing (Goncalo). Analysis . Disease projects (Sardinia, T2D). A public database of. . SNPs. . and detectable . CNVs. with allele frequency. >1. % in each of multiple human population samples. and Accurate Assembly Polishing Algorithm. Can Firtina. 1. , Jeremie S. Kim. 1,2. , Mohammed Alser. 1. , . Damla. . Senol. Cali. 2. , A. . Ercument. Cicek. 3. ,. Can Alkan. 3. , and . Onur. Mutlu. Dr. Sonalika’s Eye Clinic provide the best Low vision aids treatment in Pune, Hadapsar, Amanora, Magarpatta, Mundhwa, Kharadi Rd, Viman Nagar, Wagholi, and Wadgaon Sheri