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Sequence Analysis, Pair Wise Alignment, and Database Searching

Sequence Analysis, Pair Wise Alignment, and Database Searching

Sequence Analysis, Pair Wise Alignment, and Database Searching. Stephen Sontum Middlbury College sontum@middlebury.edu. Chapter 5: Alignments and Phylogenetic Trees Introduction to Bioinformatics by Arthur M. Lesk Papers by: Needleman and Pearson. What we hope to learn Pair-wise Alignment.

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1.31k views • 103 slides
Pairwise and Multiple Sequence Alignment Lesson 2

Pairwise and Multiple Sequence Alignment Lesson 2

Pairwise and Multiple Sequence Alignment Lesson 2. Motivation.

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813 views • 59 slides
Rationale for searching sequence databases

Rationale for searching sequence databases

Rationale for searching sequence databases. May 11, 2004 Writing projects due May 25 Quiz #3 on Thurs., May 20

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488 views • 32 slides
Chapter 3

Chapter 3

Chapter 3. Computational Molecular Biology Michael Smith msmith@cs.fit.edu. Sequence Comparison. Sequence comparison is the most important operation in computational biology Consists of finding which parts of the sequences are alike and which parts differ. Similarity and Alignment.

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304 views • 30 slides
Clustering Sequences in a Metric Space

Clustering Sequences in a Metric Space

Clustering Sequences in a Metric Space. The MoBIoS Project. Rui Mao, Daniel P. Miranker, Jacob N. Sarvela and Weijia Xu Department of Computer Sciences, University of Texas Austin, TX 78712, USA {rmao, miranker}@cs.utexas.edu

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363 views • 27 slides
Homology Search Tools

Homology Search Tools

Homology Search Tools. Kun-Mao Chao ( ??? ) Department of Computer Science and Information Engineering National Taiwan University, Taiwan WWW: http://www.csie.ntu.edu.tw/~kmchao. Homology Search Tools. Smith-Waterman (Smith and Waterman, 1981; Waterman and Eggert, 1987)

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437 views • 26 slides
Scoring Matrices for Sequence Alignment

Scoring Matrices for Sequence Alignment

Scoring Matrices for Sequence Alignment. Anne Haake Rhys Price Jones. Scoring Matrices. Sequence comparisons require some scoring matrices To use the alignment algorithms to do database searches, we need some scoring schemes that are based on biological knowledge.

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1.21k views • 23 slides
Scoring Matrices for Sequence Alignment

Scoring Matrices for Sequence Alignment

Scoring Matrices for Sequence Alignment. Anne Haake Rhys Price Jones. Scoring Matrices. Sequence comparisons require some scoring matrices To use the alignment algorithms to do database searches, we need some scoring schemes that are based on biological knowledge.

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281 views • 23 slides
Sequence Alignment III

Sequence Alignment III

Sequence Alignment III. CIS 667 February 10, 2004. Extensions to the Basic Algorithm. We have seen that the basic dynamic programming algorithm can be used to solve Global alignment Semi-global alignment Local alignment

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477 views • 18 slides
Sequence Alignment III

Sequence Alignment III

Sequence Alignment III. CIS 667 February 10, 2004. Extensions to the Basic Algorithm. We have seen that the basic dynamic programming algorithm can be used to solve Global alignment Semi-global alignment Local alignment

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297 views • 18 slides
Overview of sequence database searching techniques and multiple alignment

Overview of sequence database searching techniques and multiple alignment

Overview of sequence database searching techniques and multiple alignment. May 1, 2001 Quiz on May 3-Dynamic programming-Needleman-Wunsch method

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435 views • 14 slides
Sequence Alignments Revisited

Sequence Alignments Revisited

Sequence Alignments Revisited. Scoring nucleotide sequence alignments was easier Match score Possibly different scores for transitions and transversions For amino acids, there are many more possible substitutions

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200 views • 10 slides

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