'Genome alignment' diaporamas de présentation

Comparative Genomics Sridhar Hannenhalli sridhar@umiacs.umd

Comparative Genomics Sridhar Hannenhalli sridhar@umiacs.umd.edu. " Nothing in biology makes sense except in the light of evolution ." Theodosius Dobzhansky, 1932. What is comparative genomics.

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Application Driven Design for a Large-Scale, Multi-Purpose Grid Infrastructure

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Whole Genome Alignment

Whole Genome Alignment. Adam M Phillippy amp@cs.umd.edu. CCGGTAGGCTATTAAACGGGGTGAGGAGCGTTGGCATAGCA. CCGGTAGGCTATTAAACGGGGTGAGGAGCGTTGGCATAGCA. Goal of WGA. For two genomes, A and B , find a mapping from each position in A to its corresponding position in B. 41 bp genome.

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Tools for Comparative Sequence Analysis

Tools for Comparative Sequence Analysis. www.dcode.org. Ivan Ovcharenko Lawrence Livermore National Laboratory. A set of problems: http://www.dcode.org/bioquest.php. 1. Browsing genomes using synteny links 2. Aligning sequences to vertebrate genomes

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GMOD/GBrowse_syn

GMOD/GBrowse_syn. Sheldon McKay iPlant Collaborative DNA Learning Center Cold Spring Harbor Laboratory. Outline. A few words on whole genome alignment A brief survey of synteny browsers A few challenges of rendering comparative data Comparative genome browsing with GBrowse_syn.

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Multiple Whole Genome Alignment

Multiple Whole Genome Alignment. BMI/CS 776 www.biostat.wisc.edu/bmi776/ Spring 2019 Colin Dewey colin.dewey@wisc.edu. These slides, excluding third-party material, are licensed under CC BY-NC 4.0 by Mark Craven, Colin Dewey, and Anthony Gitter. Goals for Lecture. Key concepts

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Genome Alignment

Genome Alignment. Alignment Methods. Needleman-Wunsch (global) and Smith-Waterman (local) use dynamic programming Guaranteed to find an optimal alignment given a particular scoring function Too computationally intensive for genome alignment, especially multiple genomes. Genome Alignment.

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Short read mapping (Alignment)

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NMI Testbed GRID Utility for Virtual Organization

NMI Testbed GRID Utility for Virtual Organization. Art Vandenberg Avandenberg@gsu.edu Director, Advanced Campus Services Georgia State University. NSF Supported. This material is based in part upon work supported by the National Science Foundation under Grant No. ANI-0123937 and

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Whole Genome Alignment

Whole Genome Alignment. BMI/CS 776 www.biostat.wisc.edu/~craven/776.html Mark Craven craven@biostat.wisc.edu February 2002. Announcements. talk of interest today: Divergence Time and Evolutionary Rate Estimation with Multilocus Data Jeffrey Thorne, North Carolina State University

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MCB3895-004 Lecture # 14 Oct 21/14

MCB3895-004 Lecture # 14 Oct 21/14. Genome alignment. Genome alignment. Basic problem: align long DNA sequences to each other Difficult to do computationally efficiently Note: different from BLAST, which is designed to find homologs between a query sequence and a database

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