Local alignment - PowerPoint PPT Presentation
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.
By Jimmy
Local alignment, BLAST and Psi-BLAST
Local alignment, BLAST and Psi-BLAST. October 25, 2012 Local alignment Quiz 2 Learning objectives-Learn the basics of BLAST and Psi-BLAST Workshop-Use BLAST2 to determine local sequence similarities. Homework #6 due Nov 1 Chapter 5, Problem 8 Chapter 6, Problems 1 and 4. Local Alignment.
By ronald
Tcoffee@igs: a web server for computing, evaluating and combining multiple sequence alignments
Tcoffee@igs: a web server for computing, evaluating and combining multiple sequence alignments. Olivier Poirot, Eamonn O'Toole and Cedric Notredame Nucleic Acids Research, 31, 3503-3506 (2003) July 22, 2003 Park, Ji-Yoon. Abstract. Tcoffee@igs
By robbin
Combined Phred quality Identification
Illumina PE read two fq. Illumina PE read one fq. Failed Filter. Phred quality filtering. Combined Phred quality Identification. Phred quality Graph. Discard read. Filtering arguments. Passed Filter. Barcode Match quality and Identification. Failed Filter. Barcode quality filtering.
By oleg
CS 5263 Bioinformatics
CS 5263 Bioinformatics. Lecture 5: Affine Gap Penalties. Last lecture. Local Sequence Alignment Bounded Dynamic Programming Linear Space Sequence Alignment. The Smith-Waterman algorithm. Initialization : F(0, j) = F(i, 0) = 0 0 F(i – 1, j) – d F(i, j – 1) – d
By sirvat
Class 4: Fast Sequence Alignment
Class 4: Fast Sequence Alignment. Alignment in Real Life. One of the major uses of alignments is to find sequences in a “database” Such collections contain massive number of sequences (order of 10 6 )
By onan
Design and creation of multiple sequence alignments Unit 13
Design and creation of multiple sequence alignments Unit 13. BIOL221T : Advanced Bioinformatics for Biotechnology. Irene Gabashvili, PhD. Dot Plot (Matrix) for Sequence comparison. Reminders from Previous Lectures. DOTPLOTS. DOROTHYCROWFOOTHODGKIN. DOROTHYHODGKIN.
By jake
Class 8: Pair HMMs
Class 8: Pair HMMs. FSA HHMs: Why?. Advantages: Obtain reliability of alignment Explore alternative (sub-optimal) alignments Score similarity of sequences independent of any specific alignment. ε. W s. B q si. B (+1,+0). s ( s i ,t j ). 1 - ε. s ( s i ,t j ). δ. 1 -2 δ.
By carrie
Index-based approach to similarity search in protein and nucleotide databases
Index-based approach to similarity search in protein and nucleotide databases. David Hoksza, Tom áš Skopal Charles University in Prague Department of Software Engineering Czech Republic. Presentation Outline. Biological background Protein and nucleotide databases Current methods
By neil
PSI-BLAST and Multiple Sequence Alignments
Doug Raiford Lesson 5. PSI-BLAST and Multiple Sequence Alignments. Left off…. Dynamic programming methods Needleman-Wunsch (global alignment) Smith-Waterman (local alignment) BLAST. Fixed: best Linear: next best Polynomial (n 2 ): not bad Exponential (3 n ): very bad. But….
By gigi
Sequence Alignment (I)
Sequence Alignment (I). Kun-Mao Chao ( 趙坤茂 ) Department of Computer Science and Information Engineering National Taiwan University, Taiwan E-mail: kmchao@csie.ntu.edu.tw WWW: http://www.csie.ntu.edu.tw/~kmchao. Useful Websites. MIT Biology Hypertextbook
By elden
CS 5263 Bioinformatics
CS 5263 Bioinformatics. Lecture 4: Local Sequence Alignment, More Efficient Sequence Alignment Algorithms. Roadmap. Review of last lecture Local sequence alignment More efficient sequence alignment algorithms. Given a scoring scheme, Match: m Mismatch: -s Gap: -d
By fathia
BNFO 602 Lecture 2
BNFO 602 Lecture 2. Usman Roshan. -3 mil yrs. AAGACTT. AAGACTT. AAGACTT. AAGACTT. AAGACTT. -2 mil yrs. AAGGCTT. AAG G CTT. AAGGCTT. AAGGCTT. T_GACTT. T_GACTT. T _ GACTT. T_GACTT. -1 mil yrs. _GGGCTT. _ G GGCTT. _GGGCTT. TAGACCTT. T AG A C CTT. TAGACCTT. A _ C ACTT. A_CACTT.
By sonel
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.
By masao
Lecture 2: Gene and protein sequence alignment methods .
Lecture 2: Gene and protein sequence alignment methods. CGGATCAT—GGA CTTAACATTGAA GAGAACATAGTA. Gene and Protein Sequence Alignment as a Mathematical Problem:. Example: Sequence a: ATTCTTGC Sequence b: ATCCTATTCTAGC
By juana
生物資訊演算法
生物資訊演算法. Final presentation -. A generalized global alignment algorithm. 資訊三 B90902105 高孟駿 電機四 B89901143 李庭諭. Outline. Introduction Alignment model Algorithm ( including correctness proof ) Complexity Analysis Discussion. Motivation.
By chiara
Pairwise sequence alignment
Pairwise sequence alignment. Based on presentation by Irit Gat-Viks, which is based on presentation by Amir Mitchel, Introduction to bioinformatics course, Bioinformatics unit, Tel Aviv University. and of Benny shomer, Bar-Ilan university. Where we are in the course?.
By feryal
Why do we want to align protein sequences?
Protein Sequence Comparison Patrice Koehl http://koehllab.genomecenter.ucdavis.edu/teaching/ecs129/06/lecture-notes. Why do we want to align protein sequences?. If two sequences align well, the corresponding proteins are homologous; they probably share the same structure and/or function
By isolde
Sequence Alignment
Sequence Alignment. Complete DNA Sequences. More than 300 complete genomes have been sequenced. Evolution. Evolution at the DNA level. Deletion. Mutation. …AC GGTG CAGT T ACCA…. SEQUENCE EDITS. …AC ---- CAGT C CACCA…. REARRANGEMENTS. Inversion. Translocation. Duplication.
By anka
Sequence Alignment
Sequence Alignment. Complete DNA Sequences. More than 300 complete genomes have been sequenced. Evolution. Evolution at the DNA level. Deletion. Mutation. …AC GGTG CAGT T ACCA…. SEQUENCE EDITS. …AC ---- CAGT C CACCA…. REARRANGEMENTS. Inversion. Translocation. Duplication.
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