'Global alignment' diaporamas de présentation

Lecture 2. Optimal Sequence Alignment

Lecture 2. Optimal Sequence Alignment. The Chinese University of Hong Kong CSCI3220 Algorithms for Bioinformatics. Lecture outline. Problems related to sequences Core: Sequence alignment Sequence alignment Problem components Difficulty Methods (focused on optimal methods in this lecture)

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Ch 11 . Assessing Pairwise Sequence Similarity: BLAST and FASTA

Ch 11 . Assessing Pairwise Sequence Similarity: BLAST and FASTA. Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Third Edition . IDB Lab. Seoul National University. Contents. Introduction Global Versus Local Sequence Alignments Dotplots Scoring Matrices BLAST

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SMAWK

SMAWK. Revise. a. a. c. g. a. c. g. a. 6. 7. 3. 4. 1. 5. 2. 8. 0. c. 1. t. 2. a. 3. c. 4. g. 5. a. 6. g. 7. a. 8. Global alignment (Revise). Alignment graph for S = aacgacga , T = ctacgaga. V( i,j ) = max { V(i-1,j-1) + ?(S[ i ], T[j]),

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BLAST (I)

BLAST (I). B asic L ocal A lignment S earch T ool. ??? ?????? email: jimfann@itri.org.tw 02/26/2008. Reference & Sources. Jian Ye, Scott McGinnis, and Thomas L. Madden (2006) "BLAST: improvements for better sequence analysis" Nucleic Acids Res. July 1; 34 (Web Server issue): W6-W9

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Gene Prediction: Similarity-Based Approaches

Gene Prediction: Similarity-Based Approaches. Outline. Introduction Exon Chaining Problem Spliced Alignment Gene Prediction Tools. Section 1: Introduction. Similarity-Based Approach to Gene Prediction. Some genomes may be well-studied, with many genes having been experimentally verified.

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Building for the James Webb Space Telescope: The Near-Infrared Camera

Building for the James Webb Space Telescope: The Near-Infrared Camera. Marcia Rieke Steward Observatory 02 June 2008 American Astronomical Society, St. Louis, MO With help from the NIRCam Team:

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Blast output

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Sparse Normalized Local Alignment Nadav Efraty Gad M. Landau

Sparse Normalized Local Alignment Nadav Efraty Gad M. Landau. Background - Global similarity. LCS- Longest Common Subsequence. Background - LCS milestones. (1977) Hirschberg - Algorithms for the longest common subsequence problem.

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Last lecture summary

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Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities

Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities. 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

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Error model for massively parallel (454) DNA sequencing

Error model for massively parallel (454) DNA sequencing. Sriram Raghuraman (working with Haixu Tang and Justin Choi). Sequencing Preparation. Randomly fragment entire genome Nebulize fragments. Add adapters. Attach to DNA capture beads in water oil emulsion

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Definitions

Definitions. Optimal alignment - one that exhibits the most correspondences. It is the alignment with the highest score . May or may not be biologically meaningful.

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Global Alignment Summary

Global Alignment Summary. If Score(i, j) denotes best score to aligning A[1 : i] and B[1 : j] Score(i-1, j) + g align A[i] with GAP Score(i, j-1) + g align B[j] with GAP Score( i , j) = max Score(i-1, j-1) + m if A[i] == B[j ]

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Basic String Alignment

Basic String Alignment. Probability theory and statistics String alignment problem Basic string alignment algorithms. Author: Roel Wijgers email: rwijgers@cs.uu.nl. Probability Theory. Conditional chance: P(A|B) = P(A / B) / P(B) Independence of A and B: when P(A / B) = P(A)P(B).

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Sequence Alignment Examples

Sequence Alignment Examples. Fall 2003 Dr. Susan Bridges. Global Alignment Example. Different scoring functions can be used with any of the algorithms. For this example, use the following scoring function: Indel (add a space) -2 Match +2 Substitution -1. Global Alignment Result.

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UK Five Year Antimicrobial Resistance Strategy 2013-2018 (published 10 th September 2013)

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LAGAN and MLAGAN

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Creating a Culture of Accountability The Kimberly-Clark Health Care Journey

Creating a Culture of Accountability The Kimberly-Clark Health Care Journey . The Journey. Our case for change It starts and ends with the leader Organizational cynics Peaks and valleys. KCHC Cultural Journey . From: 2008 T. From: 2008. To: 2012. Misaligned on goals .

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BNFO 236 Smith Waterman alignment

BNFO 236 Smith Waterman alignment. Usman Roshan. Local alignment. Global alignment may not find local similarities Modification of Needleman-Wunsch yields the Smith-Watermn algorithm for local alignment Useful in motif detection, database search, short read mapping. Local alignment.

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Update on STAR AGS/RHIC Time Mtg February 18 , 2014 Bill Christie

Update on STAR AGS/RHIC Time Mtg February 18 , 2014 Bill Christie. Summary : We started looking for collisions Thursday morning (2/13/14). Determined the Global timing shift we had to make to get trigger signals into digitizer gates about 4 that afternoon.

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