'Local alignment' presentation slideshows

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.

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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?.

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Lecture 2: Gene and protein sequence alignment methods .

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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

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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

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CS 5263 Bioinformatics

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Sequence Alignment (I)

Sequence Alignment (I). Kun-Mao Chao ( ??? ) 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

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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.

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???????. Final presentation -. A generalized global alignment algorithm. ??? B90902105 ??? ??? B89901143 ???. Outline. Introduction Alignment model Algorithm ( including correctness proof ) Complexity Analysis Discussion. Motivation.

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Sequence Alignment

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Sequence Alignment

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

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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.

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Class 4: Fast Sequence Alignment

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PSI-BLAST and Multiple Sequence Alignments

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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. ?. W s. B q si. B (+1,+0). s ( s i ,t j ). 1 - ?. s ( s i ,t j ). ?. 1 -2 ?.

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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

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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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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.

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