'Gap penalty' presentation slideshows

COT 6930 HPC and Bioinformatics Pairwise Sequence Alignment (PSA)

COT 6930 HPC and Bioinformatics Pairwise Sequence Alignment (PSA). Xingquan Zhu Dept. of Computer Science and Engineering. Outline. Dynamic Programming Dot Matrix Plot FASTA BLAST. Difficulty of PSA. Consider two sequences of length n Number of possible global alignments

1.06k views • 73 slides

Using Dynamic Programming To Align Sequences

803 views • 71 slides

Lecture outline

Sequence alignment Why do we need to align sequences? Evolutionary relationships Gaps and scoring matrices Dynamic programming Global alignment (Needleman & Wunsch) Local alignment (Smith & Waterman) Database searches BLAST FASTA. Lecture outline. Complete DNA Sequences.

950 views • 70 slides

Genomics and Personalized Care in Health Systems Lecture 3 Sequence Alignment

Genomics and Personalized Care in Health Systems Lecture 3 Sequence Alignment. Leming Zhou School of Health and Rehabilitation Sciences Department of Health Information Management. Outline. Pairwise sequence alignment Multiple sequence alignment Phylogenetic tree. Similarity Search.

765 views • 64 slides

Algorithms for Alignment of Genomic Sequences

Algorithms for Alignment of Genomic Sequences. Michael Brudno Department of Computer Science Stanford University PGA Workshop 07/16/2004. Conservation Implies Function. Gene. Exon. CNS: Other Conserved. Edit Distance Model (1).

696 views • 59 slides

Pairwise sequence comparison

Pairwise sequence comparison. Prof. William Stafford Noble Department of Genome Sciences Department of Computer Science and Engineering University of Washington thabangh@gmail.com. One-minute responses. Need more clarification on the alignment of sequences.

540 views • 45 slides

Sequence Similarity

681 views • 42 slides

Examining Activity Patterns Using Fuzzy Clustering

Examining Activity Patterns Using Fuzzy Clustering. by D De Silva, University of Calgary JD Hunt, University of Calgary PROCESSUS Second International Colloquium Toronto ON, Canada June 2005. Overview. Introduction Data Method Preliminary Results Conclusions. Introduction. Context

557 views • 39 slides

Introduction to the theory of sequence alignment

Introduction to the theory of sequence alignment. Yves Moreau Master of Artificial Intelligence Katholieke Universiteit Leuven 2003-2004. References.

463 views • 38 slides

Sequence Alignment July 22, 2009

Sequence Alignment July 22, 2009. Charlie Whittaker Bioinformatics and Computing Core Facility The David H. Koch Institute for Integrative Cancer Research charliew@mit.edu http://luria.mit.edu/July_AP_2009/. Alignment and Bioinformatics . Widespread usage Sequence annotation

501 views • 35 slides

Sequence Alignment CSCE 769 Guest Lecture November 1, 2012 Stephanie Irausquin, PhD

Sequence Alignment CSCE 769 Guest Lecture November 1, 2012 Stephanie Irausquin, PhD. Sequence Alignment: Definition and Importance.

562 views • 35 slides

Alignment of Genomic Sequences

Alignment of Genomic Sequences. Wen-Hsiung Li Ecology & Evolution Univ. of Chicago. Sequence Alignment. (1) pairs of matched bases (2) pairs of mismatched bases (3) pairs consisting of a base from one sequence and a gap (null base) from the other sequence.

453 views • 34 slides

Evolution

Doug Raiford Lesson 4. Evolution. Darwinian Evolution. Parental combinations and mutational changes. Heritable traits Variation in population (parental combinations and mutations) Visible, phenotypical differences lead to different survival rates. Natural Selection. Meiosis.

435 views • 30 slides

WORKING WITH BIOSEQUENCES Alignments and similarity search

415 views • 28 slides

Algorithms for Pairwise Sequence Alignment

Algorithms for Pairwise Sequence Alignment. Craig A. Struble, Ph.D. Marquette University. Overview. Pairwise Sequence Alignment Dynamic Programming Solution Global Alignment Local Alignment BLAST and FASTA. Pairwise Sequence Alignment.

627 views • 26 slides

Class 3: Sequence similarity

Class 3: Sequence similarity. Motivation. Same gene, or similar gene Suffix of A similar to prefix of B? Suffix of A similar to prefix of B..Z? Longest similar substring of A, B Longest similar substring of A, B..Z For each, How big? How similar?. Define alignment.

331 views • 24 slides

A Brief Introduction to Biological Sequence Alignment

A Brief Introduction to Biological Sequence Alignment. Sun Kim CSE SNU For Bio Data Mining 4541.776.002 Sep 2011. Aligning a pair of sequences. Problem: given a pair of sequences, find the best alignment among all possible alignments. Goal: to compute the best alignment needs

422 views • 22 slides

Sequence comparison: Introduction and motivation

Sequence comparison: Introduction and motivation. Genome 559: Introduction to Statistical and Computational Genomics Prof. James H. Thomas. Logistics. Syllabus and web site: Should I take this class ? Grading Send homework by email ATTACHMENT.

261 views • 20 slides

Sequence Alignment

Sequence Alignment. Global Alignment : compare two sequences in their entirety; the gap penalty is assessed regardless of whether gaps are located internally within a sequence, or at the end of one or both sequences. The Needleman and Wunsch Algorithm

1.86k views • 10 slides

Needleman Wunsch Sequence Alignment

353 views • 6 slides