'Local alignment' presentation slideshows

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BNFO 236 Smith Waterman alignment

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
(724 views)

Local alignment, BLAST and Psi-BLAST

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
(404 views)

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

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
(162 views)

Combined Phred quality Identification

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
(59 views)

CS 5263 Bioinformatics

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
(115 views)

Class 4: Fast Sequence Alignment

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
(130 views)

Design and creation of multiple sequence alignments Unit 13

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
(113 views)

Class 8: Pair HMMs

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
(135 views)

Index-based approach to similarity search in protein and nucleotide databases

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
(107 views)

PSI-BLAST and Multiple Sequence Alignments

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
(172 views)

Sequence Alignment (I)

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
(121 views)

CS 5263 Bioinformatics

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
(131 views)

BNFO 602 Lecture 2

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
(102 views)

Definitions

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
(52 views)

Lecture 2: Gene and protein sequence alignment methods .

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
(107 views)

生物資訊演算法

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
(162 views)

Pairwise sequence alignment

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
(456 views)

Why do we want to align protein sequences?

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
(193 views)

Sequence Alignment

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
(134 views)

Sequence Alignment

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 melina
(104 views)

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